Starting phenix.real_space_refine
on Sat Nov 16 16:34:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_36148_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_36148.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_36148.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_36148_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbx_36148/11_2024/8jbx_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-5513/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: 7.00, per 1000 atoms: 0.59
  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: 2.88
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 5.73
  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: 4.09

  Time building geometry restraints manager: 3.33 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:             1.450
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.620
  Find NCS groups from input model:        0.260
  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:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.600
-------------------------------------------------------------------------------
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= 0.216
  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 

*********************** 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  : 0.852 
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: 0.3245
  time to fit residues: 114.3907
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  : 0.895 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
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= 0.312
  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 

*********************** 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  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8293 (pm20) cc_final: 0.8085 (pm20)
REVERT: A   76 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8654 (tm-30)
REVERT: A   87 SER cc_start: 0.9573 (p) cc_final: 0.9286 (t)
REVERT: A   94 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8510 (tp30)
REVERT: A  108 ASN cc_start: 0.9337 (t0) cc_final: 0.9070 (t0)
REVERT: B   31 LYS cc_start: 0.9491 (tttt) cc_final: 0.9188 (tttp)
REVERT: B   53 GLU cc_start: 0.8387 (tp30) cc_final: 0.7802 (tp30)
REVERT: B   84 MET cc_start: 0.8788 (tpp) cc_final: 0.8425 (tpt)
REVERT: B   92 ARG cc_start: 0.9383 (ttp80) cc_final: 0.8991 (ttp80)
REVERT: D   42 TYR cc_start: 0.7826 (t80) cc_final: 0.7321 (t80)
REVERT: D   47 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8630 (tm-30)
REVERT: D   68 ASP cc_start: 0.9231 (t0) cc_final: 0.8899 (t0)
REVERT: D   89 ILE cc_start: 0.9430 (mm) cc_final: 0.9090 (mm)
REVERT: D  105 GLU cc_start: 0.8660 (tp30) cc_final: 0.8073 (tp30)
REVERT: E   42 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8784 (ttm110)
REVERT: E   76 GLN cc_start: 0.9125 (pp30) cc_final: 0.8833 (pp30)
REVERT: E  108 ASN cc_start: 0.9618 (t0) cc_final: 0.9191 (t0)
REVERT: G   35 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8802 (mtm-85)
REVERT: G   59 THR cc_start: 0.9527 (m) cc_final: 0.9270 (t)
REVERT: G   73 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.8955 (t0)
REVERT: G  100 VAL cc_start: 0.9413 (t) cc_final: 0.9104 (p)
REVERT: G  101 THR cc_start: 0.9345 (m) cc_final: 0.9001 (t)
REVERT: H   40 TYR cc_start: 0.9066 (m-80) cc_final: 0.8811 (m-80)
REVERT: H   51 ASP cc_start: 0.8924 (p0) cc_final: 0.8717 (p0)
REVERT: H  105 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7785 (mm-30)
REVERT: H  113 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8157 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 247
  average time/residue: 0.3008
  time to fit residues: 98.6130
Evaluate side-chains
  231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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 49 optimal weight:    8.9990
   chunk 27 optimal weight:    0.2980
   chunk 74 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 96 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    3.4588

-------------------------------------------------------------------------------
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
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  12684  Z= 0.334
  Angle     :  0.632   7.157  18373  Z= 0.366
  Chirality :  0.036   0.161   2090
  Planarity :  0.004   0.041   1320
  Dihedral  : 30.970 177.415   3997
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 28.59 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.31), residues: 734
  helix:  2.00 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.92 (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   0.040   0.002   TYR D  40 
 ARG   0.008   0.001   ARG D  92 

*********************** 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
  250 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 218
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8456 (pm20) cc_final: 0.8221 (pm20)
REVERT: A   68 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.9014 (tp40)
REVERT: A   76 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8654 (tm-30)
REVERT: A   87 SER cc_start: 0.9577 (p) cc_final: 0.9291 (t)
REVERT: A   94 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8539 (tp30)
REVERT: A  108 ASN cc_start: 0.9394 (t0) cc_final: 0.9100 (t0)
REVERT: B   31 LYS cc_start: 0.9495 (tttt) cc_final: 0.9210 (tttp)
REVERT: B   53 GLU cc_start: 0.8356 (tp30) cc_final: 0.7878 (tp30)
REVERT: B   84 MET cc_start: 0.8782 (tpp) cc_final: 0.8581 (tpp)
REVERT: B   92 ARG cc_start: 0.9401 (ttp80) cc_final: 0.9107 (ttp80)
REVERT: C   61 GLU cc_start: 0.8809 (tp30) cc_final: 0.8551 (tp30)
REVERT: D   42 TYR cc_start: 0.7883 (t80) cc_final: 0.7406 (t80)
REVERT: D   47 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8704 (tm-30)
REVERT: D   68 ASP cc_start: 0.9251 (t0) cc_final: 0.8915 (t0)
REVERT: D   89 ILE cc_start: 0.9355 (mm) cc_final: 0.9085 (mm)
REVERT: D  105 GLU cc_start: 0.8641 (tp30) cc_final: 0.8375 (tp30)
REVERT: E   72 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8531 (mtt90)
REVERT: E   76 GLN cc_start: 0.9133 (pp30) cc_final: 0.8817 (pp30)
REVERT: E  108 ASN cc_start: 0.9607 (t0) cc_final: 0.9284 (t0)
REVERT: F   53 GLU cc_start: 0.8984 (tp30) cc_final: 0.8757 (tp30)
REVERT: F   63 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8646 (mt-10)
REVERT: F   85 ASP cc_start: 0.8855 (m-30) cc_final: 0.8566 (m-30)
REVERT: G   59 THR cc_start: 0.9540 (m) cc_final: 0.9220 (t)
REVERT: G   73 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.9110 (t0)
REVERT: G  100 VAL cc_start: 0.9442 (t) cc_final: 0.9150 (p)
REVERT: G  101 THR cc_start: 0.9472 (m) cc_final: 0.9115 (t)
REVERT: H   51 ASP cc_start: 0.8973 (p0) cc_final: 0.8758 (p0)
REVERT: H   59 MET cc_start: 0.9323 (tpp) cc_final: 0.9107 (mmm)
REVERT: H  113 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8182 (tm-30)
  outliers start: 32
  outliers final: 19
  residues processed: 239
  average time/residue: 0.2962
  time to fit residues: 94.6367
Evaluate side-chains
  232 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 210
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  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  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   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 67 optimal weight:    0.0010
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 94 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.0990

-------------------------------------------------------------------------------
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
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12684  Z= 0.202
  Angle     :  0.582   6.829  18373  Z= 0.342
  Chirality :  0.033   0.163   2090
  Planarity :  0.004   0.041   1320
  Dihedral  : 30.813 178.032   3997
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 29.55 %
    Favored  : 66.77 %
  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:  2.04 (0.31), residues: 734
  helix:  2.13 (0.22), residues: 535
  sheet:  None (None), residues: 0
  loop : -0.84 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.008   0.001   PHE B 100 
 TYR   0.038   0.002   TYR D  40 
 ARG   0.007   0.000   ARG D  92 

*********************** 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
  257 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 234
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8415 (pm20) cc_final: 0.8177 (pm20)
REVERT: A   60 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8802 (tp)
REVERT: A   76 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8559 (tm-30)
REVERT: A   87 SER cc_start: 0.9514 (p) cc_final: 0.9200 (t)
REVERT: A   94 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8399 (tp30)
REVERT: A  108 ASN cc_start: 0.9343 (t0) cc_final: 0.9091 (t0)
REVERT: B   31 LYS cc_start: 0.9472 (tttt) cc_final: 0.9212 (tttp)
REVERT: B   84 MET cc_start: 0.8612 (tpp) cc_final: 0.8083 (tpp)
REVERT: B   88 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7505 (m-80)
REVERT: B   92 ARG cc_start: 0.9328 (ttp80) cc_final: 0.8952 (ttp80)
REVERT: C   84 GLN cc_start: 0.9484 (tp-100) cc_final: 0.9110 (tp-100)
REVERT: C   88 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8480 (mmt90)
REVERT: D   42 TYR cc_start: 0.7776 (t80) cc_final: 0.7391 (t80)
REVERT: D   47 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8658 (tm-30)
REVERT: D   68 ASP cc_start: 0.9214 (t0) cc_final: 0.8918 (t0)
REVERT: D  105 GLU cc_start: 0.8463 (tp30) cc_final: 0.8254 (tp30)
REVERT: D  106 LEU cc_start: 0.9394 (mt) cc_final: 0.9179 (tp)
REVERT: E   68 GLN cc_start: 0.9233 (tt0) cc_final: 0.8992 (tt0)
REVERT: E   72 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (mtt90)
REVERT: E   76 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8771 (pp30)
REVERT: E  108 ASN cc_start: 0.9572 (t0) cc_final: 0.9181 (t0)
REVERT: F   53 GLU cc_start: 0.8950 (tp30) cc_final: 0.8733 (tp30)
REVERT: G   24 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8783 (mm-40)
REVERT: G   59 THR cc_start: 0.9493 (m) cc_final: 0.9184 (t)
REVERT: G   73 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.8991 (t0)
REVERT: G   75 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8952 (mmmm)
REVERT: G  100 VAL cc_start: 0.9405 (t) cc_final: 0.9104 (p)
REVERT: G  101 THR cc_start: 0.9431 (m) cc_final: 0.9097 (t)
REVERT: H   51 ASP cc_start: 0.8925 (p0) cc_final: 0.8680 (p0)
REVERT: H  113 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8204 (tm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 246
  average time/residue: 0.2898
  time to fit residues: 95.7156
Evaluate side-chains
  238 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 222
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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   66 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
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   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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**
D  63 ASN
E  93 GLN
F  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2108

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= 0.266
  Angle     :  0.604   7.429  18373  Z= 0.352
  Chirality :  0.034   0.166   2090
  Planarity :  0.004   0.036   1320
  Dihedral  : 30.906 177.750   3997
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.39 %
    Favored  : 65.18 %
  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:  2.08 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.70 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.007   0.001   PHE B 100 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.007   0.000   ARG B  95 

*********************** 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
  254 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 220
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8450 (pm20) cc_final: 0.8189 (pm20)
REVERT: A   76 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8564 (tm-30)
REVERT: A   87 SER cc_start: 0.9530 (p) cc_final: 0.9235 (t)
REVERT: A   94 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8482 (tp30)
REVERT: A  108 ASN cc_start: 0.9368 (t0) cc_final: 0.9100 (t0)
REVERT: B   31 LYS cc_start: 0.9489 (tttt) cc_final: 0.9209 (tttp)
REVERT: B   84 MET cc_start: 0.8674 (tpp) cc_final: 0.8322 (tpp)
REVERT: B   88 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7817 (m-80)
REVERT: B   92 ARG cc_start: 0.9356 (ttp80) cc_final: 0.8901 (ttp80)
REVERT: D   42 TYR cc_start: 0.7897 (t80) cc_final: 0.7534 (t80)
REVERT: D   47 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8637 (tm-30)
REVERT: D   57 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8661 (mmmm)
REVERT: D   68 ASP cc_start: 0.9217 (t0) cc_final: 0.8872 (t0)
REVERT: D   89 ILE cc_start: 0.9216 (mm) cc_final: 0.8857 (mm)
REVERT: D  105 GLU cc_start: 0.8525 (tp30) cc_final: 0.8313 (tp30)
REVERT: E   72 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8585 (mtt90)
REVERT: E   76 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8813 (pp30)
REVERT: F   53 GLU cc_start: 0.8956 (tp30) cc_final: 0.8719 (tp30)
REVERT: F   63 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8666 (mt-10)
REVERT: F   84 MET cc_start: 0.8819 (mmm) cc_final: 0.8610 (tmm)
REVERT: G   24 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8866 (mm-40)
REVERT: G   59 THR cc_start: 0.9493 (m) cc_final: 0.9178 (t)
REVERT: G   73 ASN cc_start: 0.9358 (OUTLIER) cc_final: 0.8995 (t0)
REVERT: G   90 ASP cc_start: 0.8811 (t0) cc_final: 0.8580 (t0)
REVERT: G  100 VAL cc_start: 0.9446 (t) cc_final: 0.9176 (p)
REVERT: H   51 ASP cc_start: 0.8947 (p0) cc_final: 0.8692 (p0)
REVERT: H  113 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8173 (tm-30)
  outliers start: 34
  outliers final: 19
  residues processed: 239
  average time/residue: 0.2886
  time to fit residues: 92.3293
Evaluate side-chains
  233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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   74 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  126 LEU
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   88 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  102 ILE
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   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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  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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12684  Z= 0.232
  Angle     :  0.595   6.967  18373  Z= 0.347
  Chirality :  0.034   0.163   2090
  Planarity :  0.004   0.033   1320
  Dihedral  : 30.856 177.746   3997
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 29.55 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.31), residues: 734
  helix:  2.07 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.61 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.007   0.001   PHE B 100 
 TYR   0.017   0.002   TYR D  40 
 ARG   0.007   0.000   ARG H  92 

*********************** 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
  247 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 221
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8353 (pm20) cc_final: 0.8096 (pm20)
REVERT: A   87 SER cc_start: 0.9513 (p) cc_final: 0.9209 (t)
REVERT: A   94 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8449 (tp30)
REVERT: A  108 ASN cc_start: 0.9339 (t0) cc_final: 0.9097 (t0)
REVERT: A  123 ASP cc_start: 0.8651 (m-30) cc_final: 0.8319 (m-30)
REVERT: B   31 LYS cc_start: 0.9479 (tttt) cc_final: 0.9195 (tttp)
REVERT: B   84 MET cc_start: 0.8582 (tpp) cc_final: 0.8286 (tpp)
REVERT: B   88 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (m-80)
REVERT: B   92 ARG cc_start: 0.9307 (ttp80) cc_final: 0.8867 (ttp80)
REVERT: D   42 TYR cc_start: 0.7879 (t80) cc_final: 0.7542 (t80)
REVERT: D   47 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8674 (tm-30)
REVERT: D   68 ASP cc_start: 0.9208 (t0) cc_final: 0.8856 (t0)
REVERT: D  105 GLU cc_start: 0.8525 (tp30) cc_final: 0.8305 (tp30)
REVERT: E   72 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (mtt90)
REVERT: E   76 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8818 (pp30)
REVERT: E  125 GLN cc_start: 0.8877 (mt0) cc_final: 0.8665 (mt0)
REVERT: F   53 GLU cc_start: 0.8926 (tp30) cc_final: 0.8704 (tp30)
REVERT: G   24 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8813 (mm-40)
REVERT: G   35 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8812 (mtm-85)
REVERT: G   73 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.8966 (t0)
REVERT: G  100 VAL cc_start: 0.9429 (t) cc_final: 0.9174 (p)
REVERT: H   51 ASP cc_start: 0.8945 (p0) cc_final: 0.8687 (p0)
REVERT: H  113 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8134 (tm-30)
  outliers start: 26
  outliers final: 17
  residues processed: 234
  average time/residue: 0.2900
  time to fit residues: 91.2540
Evaluate side-chains
  234 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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   71 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
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 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 10 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0470
   chunk 57 optimal weight:    0.6980
   chunk 43 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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  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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12684  Z= 0.191
  Angle     :  0.592   9.401  18373  Z= 0.343
  Chirality :  0.033   0.162   2090
  Planarity :  0.004   0.034   1320
  Dihedral  : 30.731 177.852   3997
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 32.27 %
    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:  2.13 (0.32), residues: 734
  helix:  2.09 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.58 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.018   0.002   TYR H  40 
 ARG   0.007   0.000   ARG H  92 

*********************** 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
  253 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 234
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8348 (pm20) cc_final: 0.8073 (pm20)
REVERT: A   60 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8551 (tp)
REVERT: A   68 GLN cc_start: 0.9177 (tt0) cc_final: 0.8944 (tt0)
REVERT: A   87 SER cc_start: 0.9468 (p) cc_final: 0.9152 (t)
REVERT: A  108 ASN cc_start: 0.9310 (t0) cc_final: 0.9073 (t0)
REVERT: B   53 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7355 (tm-30)
REVERT: B   84 MET cc_start: 0.8497 (tpp) cc_final: 0.8221 (tpp)
REVERT: B   92 ARG cc_start: 0.9312 (ttp80) cc_final: 0.8918 (ttp80)
REVERT: C   61 GLU cc_start: 0.8678 (tp30) cc_final: 0.8170 (tp30)
REVERT: C   68 ASN cc_start: 0.9331 (t0) cc_final: 0.9113 (t0)
REVERT: D   42 TYR cc_start: 0.7796 (t80) cc_final: 0.7436 (t80)
REVERT: D   47 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8752 (tm-30)
REVERT: D   68 ASP cc_start: 0.9195 (t0) cc_final: 0.8867 (t0)
REVERT: D  105 GLU cc_start: 0.8424 (tp30) cc_final: 0.8213 (tp30)
REVERT: E   76 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8799 (pp30)
REVERT: E   79 LYS cc_start: 0.8915 (tttp) cc_final: 0.8600 (tttm)
REVERT: F   53 GLU cc_start: 0.8857 (tp30) cc_final: 0.8617 (tp30)
REVERT: F   63 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8607 (mt-10)
REVERT: F   74 GLU cc_start: 0.8895 (tp30) cc_final: 0.8514 (tp30)
REVERT: G   73 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.9011 (t0)
REVERT: G  100 VAL cc_start: 0.9398 (t) cc_final: 0.9115 (p)
REVERT: H   51 ASP cc_start: 0.8883 (p0) cc_final: 0.8577 (p0)
REVERT: H  105 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8017 (mm-30)
REVERT: H  113 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8266 (tm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 240
  average time/residue: 0.2796
  time to fit residues: 91.9528
Evaluate side-chains
  231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 217
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
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   81 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12684  Z= 0.295
  Angle     :  0.632   7.501  18373  Z= 0.365
  Chirality :  0.035   0.234   2090
  Planarity :  0.004   0.046   1320
  Dihedral  : 30.981 177.458   3997
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 32.11 %
    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:  2.05 (0.31), residues: 734
  helix:  2.01 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.54 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE C  25 
 TYR   0.023   0.002   TYR H  40 
 ARG   0.007   0.000   ARG H  33 

*********************** 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
  239 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8390 (pm20) cc_final: 0.8103 (pm20)
REVERT: A   87 SER cc_start: 0.9529 (p) cc_final: 0.9205 (t)
REVERT: A  108 ASN cc_start: 0.9379 (t0) cc_final: 0.9113 (t0)
REVERT: A  133 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8131 (pm20)
REVERT: B   31 LYS cc_start: 0.9448 (tttt) cc_final: 0.9243 (tttp)
REVERT: B   53 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: B   84 MET cc_start: 0.8667 (tpp) cc_final: 0.8384 (tpp)
REVERT: B   92 ARG cc_start: 0.9280 (ttp80) cc_final: 0.8813 (ttp80)
REVERT: D   42 TYR cc_start: 0.7824 (t80) cc_final: 0.7547 (t80)
REVERT: D   47 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8668 (tm-30)
REVERT: D   68 ASP cc_start: 0.9230 (t0) cc_final: 0.8864 (t0)
REVERT: E   72 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8576 (mtt90)
REVERT: E   76 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8832 (pp30)
REVERT: E   79 LYS cc_start: 0.8990 (tttp) cc_final: 0.8757 (tttp)
REVERT: F   63 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8625 (mt-10)
REVERT: F   74 GLU cc_start: 0.8929 (tp30) cc_final: 0.8559 (tp30)
REVERT: G   24 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8580 (mp10)
REVERT: G   59 THR cc_start: 0.9583 (m) cc_final: 0.9380 (t)
REVERT: G   73 ASN cc_start: 0.9304 (OUTLIER) cc_final: 0.8990 (t0)
REVERT: G  100 VAL cc_start: 0.9454 (t) cc_final: 0.9143 (p)
REVERT: G  101 THR cc_start: 0.9491 (m) cc_final: 0.9156 (t)
REVERT: H   51 ASP cc_start: 0.9004 (p0) cc_final: 0.8698 (p0)
REVERT: H  113 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8102 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 230
  average time/residue: 0.2774
  time to fit residues: 87.1992
Evaluate side-chains
  231 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 213
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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  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   66 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 88 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0020
   chunk 38 optimal weight:    0.7980
   chunk 69 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    3.3594

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  12684  Z= 0.332
  Angle     :  0.658   8.668  18373  Z= 0.377
  Chirality :  0.036   0.167   2090
  Planarity :  0.004   0.036   1320
  Dihedral  : 31.076 177.188   3997
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 33.07 %
    Favored  : 63.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.31), residues: 734
  helix:  2.03 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.77 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS D 109 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.026   0.003   TYR H  40 
 ARG   0.007   0.000   ARG H  33 

*********************** 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
  234 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 212
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8552 (pm20) cc_final: 0.8266 (pm20)
REVERT: A   87 SER cc_start: 0.9539 (p) cc_final: 0.9270 (t)
REVERT: A  108 ASN cc_start: 0.9439 (t0) cc_final: 0.9147 (t0)
REVERT: A  133 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8157 (pm20)
REVERT: B   31 LYS cc_start: 0.9453 (tttt) cc_final: 0.9223 (tttp)
REVERT: B   53 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: B   84 MET cc_start: 0.8739 (tpp) cc_final: 0.8526 (tpp)
REVERT: B   92 ARG cc_start: 0.9311 (ttp80) cc_final: 0.8965 (ttp80)
REVERT: D   42 TYR cc_start: 0.7909 (t80) cc_final: 0.7649 (t80)
REVERT: D   47 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8705 (tm-30)
REVERT: D   68 ASP cc_start: 0.9253 (t0) cc_final: 0.8886 (t0)
REVERT: D  105 GLU cc_start: 0.8570 (tp30) cc_final: 0.8240 (tp30)
REVERT: E   72 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8555 (mtt90)
REVERT: E   76 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8872 (pp30)
REVERT: E   79 LYS cc_start: 0.9020 (tttp) cc_final: 0.8700 (tttm)
REVERT: E  109 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9435 (mp)
REVERT: F   63 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8695 (mt-10)
REVERT: F   72 TYR cc_start: 0.8963 (m-80) cc_final: 0.8760 (m-80)
REVERT: F   74 GLU cc_start: 0.8948 (tp30) cc_final: 0.8531 (tp30)
REVERT: G   24 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8797 (mm110)
REVERT: G   59 THR cc_start: 0.9567 (m) cc_final: 0.9327 (t)
REVERT: G   73 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9001 (t0)
REVERT: G  100 VAL cc_start: 0.9449 (t) cc_final: 0.9133 (p)
REVERT: G  101 THR cc_start: 0.9516 (m) cc_final: 0.9155 (t)
REVERT: H   51 ASP cc_start: 0.9028 (p0) cc_final: 0.8710 (p0)
REVERT: H  113 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8258 (tm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 229
  average time/residue: 0.3059
  time to fit residues: 95.2003
Evaluate side-chains
  225 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 206
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  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 C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   49 LEU
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 H residue   98 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12684  Z= 0.207
  Angle     :  0.629   8.639  18373  Z= 0.360
  Chirality :  0.034   0.166   2090
  Planarity :  0.004   0.035   1320
  Dihedral  : 30.873 177.736   3997
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 32.43 %
    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:  1.92 (0.31), residues: 734
  helix:  1.89 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.50 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H  82 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.025   0.002   TYR B  88 
 ARG   0.009   0.000   ARG H  92 

********************** 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
  246 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 228
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8480 (pm20) cc_final: 0.8183 (pm20)
REVERT: A   60 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8449 (tp)
REVERT: A   87 SER cc_start: 0.9477 (p) cc_final: 0.9165 (t)
REVERT: A  108 ASN cc_start: 0.9351 (t0) cc_final: 0.9060 (t0)
REVERT: B   25 ASN cc_start: 0.8882 (t0) cc_final: 0.8664 (t0)
REVERT: B   31 LYS cc_start: 0.9417 (tttt) cc_final: 0.9210 (tttp)
REVERT: B   53 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7409 (tm-30)
REVERT: B   84 MET cc_start: 0.8514 (tpp) cc_final: 0.8263 (tpt)
REVERT: B   92 ARG cc_start: 0.9251 (ttp80) cc_final: 0.8762 (ttp80)
REVERT: D   42 TYR cc_start: 0.7753 (t80) cc_final: 0.7532 (t80)
REVERT: D   47 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8682 (tm-30)
REVERT: D   68 ASP cc_start: 0.9195 (t0) cc_final: 0.8881 (t0)
REVERT: D  105 GLU cc_start: 0.8441 (tp30) cc_final: 0.8039 (tp30)
REVERT: E   72 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8536 (mtt-85)
REVERT: E   76 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8863 (pp30)
REVERT: E   79 LYS cc_start: 0.8891 (tttp) cc_final: 0.8522 (tttm)
REVERT: F   74 GLU cc_start: 0.8894 (tp30) cc_final: 0.8409 (tp30)
REVERT: F   77 LYS cc_start: 0.9093 (mttp) cc_final: 0.8861 (mmtm)
REVERT: G   24 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8657 (mp10)
REVERT: G   59 THR cc_start: 0.9529 (m) cc_final: 0.9302 (t)
REVERT: G   73 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8987 (t0)
REVERT: G   95 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9166 (ttmm)
REVERT: G  100 VAL cc_start: 0.9401 (t) cc_final: 0.9112 (p)
REVERT: H   51 ASP cc_start: 0.8934 (p0) cc_final: 0.8570 (p0)
REVERT: H  113 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8210 (tm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 236
  average time/residue: 0.2767
  time to fit residues: 88.9174
Evaluate side-chains
  235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 221
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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 C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue   76 GLN
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 H residue   98 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 77 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0040
   chunk 14 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0670
   overall best weight:    0.5534

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.060284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.045506 restraints weight = 45882.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.55
r_work: 0.2707 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12684  Z= 0.201
  Angle     :  0.629   8.891  18373  Z= 0.359
  Chirality :  0.033   0.167   2090
  Planarity :  0.004   0.035   1320
  Dihedral  : 30.803 177.697   3997
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 33.23 %
    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:  2.07 (0.32), residues: 734
  helix:  2.00 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.43 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.031   0.002   TYR B  88 
 ARG   0.008   0.000   ARG H  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2521.07 seconds
wall clock time: 46 minutes 28.37 seconds (2788.37 seconds total)