Starting phenix.real_space_refine
on Tue Jul 29 19:53:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g86_29837/07_2025/8g86_29837.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     290      5.49       5
     S      12      5.16       5
     C    6637      2.51       5
     N    2229      2.21       5
     O    2804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11972
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2995
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 8.84, per 1000 atoms: 0.74
  Number of scatterers: 11972
  At special positions: 0
  Unit cell: (74.865, 116.725, 114.31, 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      12     16.00
     P     290     15.00
     O    2804      8.00
     N    2229      7.00
     C    6637      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: 3.90
  Conformation dependent library (CDL) restraints added in 918.9 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1424

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 2.9% beta
      134 base pairs and 275 stacking pairs defined.
    Time for finding SS restraints: 6.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.145A  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
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.236A  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 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 122
    Processing helix  chain 'E' and resid 44 through 55
    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
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.829A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    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 73
      removed outlier: 4.387A  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 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.003A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.691A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.144A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.769A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.764A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.057A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    417 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      319 hydrogen bonds
      634 hydrogen bond angles
      0 basepair planarities
      134 basepair parallelities
      275 stacking parallelities
  Total time for adding SS restraints: 4.68

  Time building geometry restraints manager: 3.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2227
        1.33 -     1.45: 4184
        1.45 -     1.57: 5764
        1.57 -     1.69: 578
        1.69 -     1.81: 22
  Bond restraints: 12775
  Sorted by residual:
  bond pdb=" C3'  DT I  20 "
       pdb=" O3'  DT I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" C3'  DT J  41 "
       pdb=" C2'  DT J  41 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.20e-01
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.449 -0.027 3.00e-02 1.11e+03 8.07e-01
  bond pdb=" C3'  DC I -22 "
       pdb=" C2'  DC I -22 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 8.00e-01
  bond pdb=" C3'  DG I  68 "
       pdb=" C2'  DG I  68 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 7.94e-01
  ... (remaining 12770 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 17993
        1.41 -     2.83: 482
        2.83 -     4.24: 14
        4.24 -     5.65: 6
        5.65 -     7.06: 3
  Bond angle restraints: 18498
  Sorted by residual:
  angle pdb=" N   GLY D 101 "
        pdb=" CA  GLY D 101 "
        pdb=" C   GLY D 101 "
      ideal   model   delta    sigma   weight residual
     113.18  118.43   -5.25 2.37e+00 1.78e-01 4.91e+00
  angle pdb=" CA  LEU F  22 "
        pdb=" CB  LEU F  22 "
        pdb=" CG  LEU F  22 "
      ideal   model   delta    sigma   weight residual
     116.30  123.36   -7.06 3.50e+00 8.16e-02 4.07e+00
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  117.81   -4.63 2.37e+00 1.78e-01 3.82e+00
  angle pdb=" C3'  DA I  29 "
        pdb=" C2'  DA I  29 "
        pdb=" C1'  DA I  29 "
      ideal   model   delta    sigma   weight residual
     101.60  104.30   -2.70 1.50e+00 4.44e-01 3.24e+00
  angle pdb=" C3'  DT I  20 "
        pdb=" O3'  DT I  20 "
        pdb=" P    DG I  21 "
      ideal   model   delta    sigma   weight residual
     120.20  122.87   -2.67 1.50e+00 4.44e-01 3.17e+00
  ... (remaining 18493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.88: 5664
       35.88 -    71.77: 1344
       71.77 -   107.65: 13
      107.65 -   143.53: 0
      143.53 -   179.41: 1
  Dihedral angle restraints: 7022
    sinusoidal: 4817
      harmonic: 2205
  Sorted by residual:
  dihedral pdb=" C4'  DT I  20 "
           pdb=" C3'  DT I  20 "
           pdb=" O3'  DT I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.41 -179.41     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ASP A  77 "
           pdb=" CB  ASP A  77 "
           pdb=" CG  ASP A  77 "
           pdb=" OD1 ASP A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.37   58.37     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CB  GLU F  74 "
           pdb=" CG  GLU F  74 "
           pdb=" CD  GLU F  74 "
           pdb=" OE1 GLU F  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.78   88.78     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 7019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1457
       0.026 -    0.052: 505
       0.052 -    0.078: 103
       0.078 -    0.104: 24
       0.104 -    0.130: 20
  Chirality restraints: 2109
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 2106 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.57e+00
        pdb=" N   PRO G  80 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO C  80 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO A  66 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2611
        2.81 -     3.33: 10262
        3.33 -     3.85: 24101
        3.85 -     4.38: 30291
        4.38 -     4.90: 40295
  Nonbonded interactions: 107560
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NH1 ARG E  72 "
            pdb=" OP1  DT J -23 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" NH2 ARG C  20 "
            pdb=" OP1  DC I -42 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O2   DC I -42 "
            pdb=" N2   DG J  42 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" O2   DC I -51 "
            pdb=" N2   DG J  51 "
     model   vdw
     2.425 2.496
  ... (remaining 107555 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' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = (chain 'F' and resid 22 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  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:             3.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     35.590
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.060
  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:12.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
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      :  0.003   0.038  12775  Z= 0.153
  Angle     :  0.502   7.065  18498  Z= 0.305
  Chirality :  0.029   0.130   2109
  Planarity :  0.003   0.047   1335
  Dihedral  : 27.264 179.413   5598
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 16.30 %
    Favored  : 82.75 %
  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:  1.60 (0.28), residues: 743
  helix:  1.47 (0.20), residues: 551
  sheet:  None (None), residues: 0
  loop :  0.04 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.010   0.001   TYR B  51 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23805 (  736)
  hydrogen bonds       : angle       8.65357 ( 1861)
  covalent geometry    : bond        0.00326 (12775)
  covalent geometry    : angle       0.50160 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7789 (mtp85)
REVERT: A  120 MET cc_start: 0.8545 (mtt) cc_final: 0.8326 (mtp)
REVERT: B   79 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8095 (mtmm)
REVERT: C  110 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0)
REVERT: D   73 GLU cc_start: 0.8617 (tp30) cc_final: 0.8383 (tp30)
REVERT: D  113 LYS cc_start: 0.8106 (ttmp) cc_final: 0.7756 (ttpp)
REVERT: E   59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7844 (pm20)
REVERT: F   27 GLN cc_start: 0.8276 (mm110) cc_final: 0.7981 (mm110)
REVERT: G   15 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6751 (tttt)
REVERT: G   71 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6668 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7803 (mmtp)
REVERT: H   54 LYS cc_start: 0.8614 (tptt) cc_final: 0.8385 (mmmm)
  outliers start: 6
  outliers final: 2
  residues processed: 163
  average time/residue: 2.0388
  time to fit residues: 349.0052
Evaluate side-chains
  142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.176328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134657 restraints weight = 10508.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 0.92
r_work: 0.3376 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12775  Z= 0.223
  Angle     :  0.628   8.107  18498  Z= 0.376
  Chirality :  0.037   0.148   2109
  Planarity :  0.005   0.042   1335
  Dihedral  : 30.866 178.974   4097
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 15.66 %
    Favored  : 80.06 %
  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:  2.44 (0.29), residues: 743
  helix:  2.18 (0.21), residues: 557
  sheet:  None (None), residues: 0
  loop : -0.09 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.014   0.002   TYR B  51 
 ARG   0.006   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06343 (  736)
  hydrogen bonds       : angle       3.18374 ( 1861)
  covalent geometry    : bond        0.00492 (12775)
  covalent geometry    : angle       0.62837 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8541 (pm20) cc_final: 0.8331 (pm20)
REVERT: A  131 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7462 (mtp180)
REVERT: B   79 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8415 (mtmm)
REVERT: C   36 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8259 (mmpt)
REVERT: D  102 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7440 (tp30)
REVERT: D  113 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7966 (tttm)
REVERT: E   59 GLU cc_start: 0.8496 (pm20) cc_final: 0.8179 (pm20)
REVERT: F   27 GLN cc_start: 0.8548 (mm110) cc_final: 0.8237 (mm110)
REVERT: F   77 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8156 (mtpt)
REVERT: F   93 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7742 (mt0)
REVERT: G   15 LYS cc_start: 0.7607 (mtpt) cc_final: 0.6897 (tttt)
REVERT: G   71 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6974 (ttm-80)
REVERT: G   75 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8195 (mmtt)
REVERT: G   95 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8393 (tmtm)
  outliers start: 27
  outliers final: 9
  residues processed: 165
  average time/residue: 2.0063
  time to fit residues: 347.9183
Evaluate side-chains
  161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  102 GLU
Chi-restraints excluded: chain D residue  113 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 76 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C  24 GLN
C 104 GLN
D  44 GLN
E  76 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.173842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.130859 restraints weight = 10786.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 0.94
r_work: 0.3318 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  12775  Z= 0.271
  Angle     :  0.650   8.417  18498  Z= 0.386
  Chirality :  0.039   0.162   2109
  Planarity :  0.005   0.042   1335
  Dihedral  : 30.949 176.854   4097
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.82 %
    Favored  : 80.38 %
  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:  2.34 (0.29), residues: 743
  helix:  2.12 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.19 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.015   0.002   PHE A  67 
 TYR   0.013   0.002   TYR B  51 
 ARG   0.006   0.001   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07199 (  736)
  hydrogen bonds       : angle       3.22499 ( 1861)
  covalent geometry    : bond        0.00611 (12775)
  covalent geometry    : angle       0.64962 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.806 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8532 (pm20) cc_final: 0.8302 (pm20)
REVERT: A  131 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7531 (mtp180)
REVERT: B   52 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7720 (mp0)
REVERT: B   79 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8405 (mtmm)
REVERT: C   36 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8212 (mmpt)
REVERT: C   92 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: D  102 GLU cc_start: 0.7739 (tp30) cc_final: 0.7425 (mm-30)
REVERT: D  113 LYS cc_start: 0.8615 (ttmp) cc_final: 0.8064 (tttm)
REVERT: E   59 GLU cc_start: 0.8448 (pm20) cc_final: 0.8189 (pm20)
REVERT: E  133 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7167 (mt-10)
REVERT: F   27 GLN cc_start: 0.8601 (mm110) cc_final: 0.8359 (mm110)
REVERT: F   77 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8108 (mtpt)
REVERT: F   93 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8151 (mt0)
REVERT: G   15 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7018 (tttt)
REVERT: G   71 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7315 (ttm110)
REVERT: G   75 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8207 (mmtt)
REVERT: G   95 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8447 (tmtm)
  outliers start: 24
  outliers final: 10
  residues processed: 150
  average time/residue: 2.0816
  time to fit residues: 327.5427
Evaluate side-chains
  155 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   84 MET
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 28 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
E  76 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.176208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.133578 restraints weight = 10683.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 0.91
r_work: 0.3353 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12775  Z= 0.169
  Angle     :  0.588   6.650  18498  Z= 0.356
  Chirality :  0.034   0.132   2109
  Planarity :  0.004   0.037   1335
  Dihedral  : 30.898 176.702   4097
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.93 %
    Favored  : 80.22 %
  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:  2.58 (0.29), residues: 743
  helix:  2.31 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  75 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.013   0.001   TYR B  51 
 ARG   0.005   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05747 (  736)
  hydrogen bonds       : angle       3.16759 ( 1861)
  covalent geometry    : bond        0.00358 (12775)
  covalent geometry    : angle       0.58849 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8531 (pm20) cc_final: 0.8312 (pm20)
REVERT: A  131 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7570 (mtp180)
REVERT: B   52 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7662 (mp0)
REVERT: B   79 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8440 (mtmm)
REVERT: C   36 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8200 (mmpt)
REVERT: C   92 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7952 (mt-10)
REVERT: D  102 GLU cc_start: 0.7668 (tp30) cc_final: 0.7426 (tp30)
REVERT: D  113 LYS cc_start: 0.8602 (ttmp) cc_final: 0.8030 (tttm)
REVERT: F   27 GLN cc_start: 0.8611 (mm110) cc_final: 0.8273 (mm110)
REVERT: F   77 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8077 (mtpt)
REVERT: F   93 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.8033 (mt0)
REVERT: G   15 LYS cc_start: 0.7662 (mtpt) cc_final: 0.6903 (tttt)
REVERT: G   75 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8168 (mmtt)
REVERT: G   95 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8403 (tmtm)
REVERT: H  105 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7625 (mmtt)
  outliers start: 18
  outliers final: 10
  residues processed: 154
  average time/residue: 1.9924
  time to fit residues: 322.2904
Evaluate side-chains
  159 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   77 ASP
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 53 optimal weight:    0.0870
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 74 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0270
   overall best weight:    0.9820

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
E  68 GLN
E  76 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.176871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.134373 restraints weight = 10756.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 0.91
r_work: 0.3360 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12775  Z= 0.169
  Angle     :  0.577   7.298  18498  Z= 0.348
  Chirality :  0.033   0.135   2109
  Planarity :  0.004   0.052   1335
  Dihedral  : 30.734 178.118   4096
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.46 %
    Favored  : 80.70 %
  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:  2.73 (0.29), residues: 743
  helix:  2.43 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.14 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.014   0.002   PHE A  67 
 TYR   0.011   0.001   TYR G  57 
 ARG   0.003   0.000   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  736)
  hydrogen bonds       : angle       3.00029 ( 1861)
  covalent geometry    : bond        0.00367 (12775)
  covalent geometry    : angle       0.57662 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 1.591 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8508 (pm20) cc_final: 0.8286 (pm20)
REVERT: A  131 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7518 (mtp180)
REVERT: B   52 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7646 (mp0)
REVERT: B   79 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8429 (mtmm)
REVERT: C   36 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8217 (mmpt)
REVERT: C   92 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: D  113 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8019 (tttm)
REVERT: E  133 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6896 (mt-10)
REVERT: F   27 GLN cc_start: 0.8635 (mm110) cc_final: 0.8299 (mm110)
REVERT: F   77 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8086 (mtpt)
REVERT: G   15 LYS cc_start: 0.7698 (mtpt) cc_final: 0.6943 (tttt)
REVERT: G   71 ARG cc_start: 0.7594 (tmm-80) cc_final: 0.7111 (ttp80)
REVERT: G   75 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8156 (mmtt)
REVERT: G   95 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8390 (tmtm)
  outliers start: 18
  outliers final: 7
  residues processed: 152
  average time/residue: 2.3600
  time to fit residues: 378.0060
Evaluate side-chains
  156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  113 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0030
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.7996

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
E  68 GLN
E  76 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.175638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.132816 restraints weight = 10796.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 0.93
r_work: 0.3343 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12775  Z= 0.206
  Angle     :  0.593   7.453  18498  Z= 0.356
  Chirality :  0.035   0.135   2109
  Planarity :  0.004   0.042   1335
  Dihedral  : 30.685 177.692   4096
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.93 %
    Favored  : 80.38 %
  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:  2.66 (0.29), residues: 743
  helix:  2.37 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.14 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.011   0.002   TYR B  51 
 ARG   0.007   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05828 (  736)
  hydrogen bonds       : angle       3.00950 ( 1861)
  covalent geometry    : bond        0.00458 (12775)
  covalent geometry    : angle       0.59261 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 1.070 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8527 (pm20) cc_final: 0.8286 (pm20)
REVERT: A  131 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7502 (mtp180)
REVERT: B   52 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7698 (mp0)
REVERT: B   79 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8413 (mtmm)
REVERT: C   36 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8225 (mmpt)
REVERT: C   92 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8006 (mt-10)
REVERT: D   82 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8265 (mtmm)
REVERT: D  105 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7860 (mtpt)
REVERT: E  115 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8326 (mppt)
REVERT: F   77 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8121 (mtpt)
REVERT: F   93 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7791 (mt0)
REVERT: G   15 LYS cc_start: 0.7698 (mtpt) cc_final: 0.6939 (tttt)
REVERT: G   75 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8165 (mmtt)
REVERT: G   95 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8388 (tmtm)
  outliers start: 17
  outliers final: 8
  residues processed: 155
  average time/residue: 2.0347
  time to fit residues: 331.3100
Evaluate side-chains
  160 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   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  76 GLN
C 104 GLN
D  44 GLN
E  68 GLN
E  76 GLN
F  27 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.175792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.132833 restraints weight = 10806.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 0.93
r_work: 0.3342 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12775  Z= 0.206
  Angle     :  0.593   7.546  18498  Z= 0.355
  Chirality :  0.035   0.130   2109
  Planarity :  0.004   0.043   1335
  Dihedral  : 30.692 177.399   4096
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.09 %
    Favored  : 80.06 %
  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:  2.66 (0.29), residues: 743
  helix:  2.34 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.03 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.014   0.002   PHE A  67 
 TYR   0.011   0.002   TYR F  51 
 ARG   0.008   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05778 (  736)
  hydrogen bonds       : angle       2.99902 ( 1861)
  covalent geometry    : bond        0.00456 (12775)
  covalent geometry    : angle       0.59294 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8535 (pm20) cc_final: 0.8302 (pm20)
REVERT: A  131 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7524 (mtp180)
REVERT: B   52 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7676 (mp0)
REVERT: B   79 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8412 (mtmm)
REVERT: C   36 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8218 (mmpt)
REVERT: C   92 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: D   73 GLU cc_start: 0.8619 (tp30) cc_final: 0.8334 (tp30)
REVERT: D   82 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8288 (mtmm)
REVERT: D  105 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7894 (mtpt)
REVERT: E  133 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6918 (mt-10)
REVERT: F   27 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8294 (mm110)
REVERT: F   77 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8118 (mtpt)
REVERT: F   93 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7809 (mt0)
REVERT: G   15 LYS cc_start: 0.7717 (mtpt) cc_final: 0.6966 (tttt)
REVERT: G   75 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8184 (mmtt)
REVERT: G   95 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8437 (tmtm)
  outliers start: 18
  outliers final: 9
  residues processed: 157
  average time/residue: 2.1898
  time to fit residues: 362.2357
Evaluate side-chains
  160 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
D  44 GLN
E  68 GLN
E  76 GLN
H  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.175138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.133626 restraints weight = 10704.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 0.93
r_work: 0.3359 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12775  Z= 0.223
  Angle     :  0.610   7.461  18498  Z= 0.364
  Chirality :  0.036   0.137   2109
  Planarity :  0.004   0.043   1335
  Dihedral  : 30.831 176.257   4096
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.46 %
    Favored  : 80.38 %
  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:  2.55 (0.29), residues: 743
  helix:  2.27 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.11 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.013   0.002   TYR B  51 
 ARG   0.008   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06195 (  736)
  hydrogen bonds       : angle       3.04443 ( 1861)
  covalent geometry    : bond        0.00499 (12775)
  covalent geometry    : angle       0.61032 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8531 (pm20) cc_final: 0.8289 (pm20)
REVERT: A  131 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7552 (mtp180)
REVERT: B   52 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7702 (mp0)
REVERT: B   79 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8435 (mtmm)
REVERT: C   36 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8235 (mmpt)
REVERT: C   92 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: D   82 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8308 (mtmm)
REVERT: E  115 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8274 (mppt)
REVERT: F   27 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8324 (mm110)
REVERT: F   77 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8153 (mtpt)
REVERT: F   93 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7788 (mt0)
REVERT: G   15 LYS cc_start: 0.7689 (mtpt) cc_final: 0.6946 (tttt)
REVERT: G   75 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8147 (mmtm)
REVERT: G   95 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8409 (tmtm)
  outliers start: 20
  outliers final: 8
  residues processed: 155
  average time/residue: 2.1064
  time to fit residues: 342.4170
Evaluate side-chains
  159 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Chi-restraints excluded: chain H residue  109 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
D  44 GLN
E  68 GLN
E  76 GLN
H  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.176605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135237 restraints weight = 10643.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 0.91
r_work: 0.3381 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12775  Z= 0.161
  Angle     :  0.582   7.642  18498  Z= 0.350
  Chirality :  0.033   0.127   2109
  Planarity :  0.004   0.040   1335
  Dihedral  : 30.812 176.665   4096
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.93 %
    Favored  : 80.22 %
  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:  2.72 (0.29), residues: 743
  helix:  2.41 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.09 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.012   0.002   TYR H  80 
 ARG   0.007   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05491 (  736)
  hydrogen bonds       : angle       3.01591 ( 1861)
  covalent geometry    : bond        0.00341 (12775)
  covalent geometry    : angle       0.58215 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8522 (pm20) cc_final: 0.8272 (pm20)
REVERT: A  131 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7552 (mtp180)
REVERT: B   52 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7631 (mp0)
REVERT: B   79 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8441 (mtmm)
REVERT: C   36 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8212 (mmpt)
REVERT: C   92 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7952 (mt-10)
REVERT: C  110 ASN cc_start: 0.8689 (t0) cc_final: 0.8297 (t0)
REVERT: D   82 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8250 (mtmm)
REVERT: E  115 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8248 (mppt)
REVERT: F   27 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8263 (mm110)
REVERT: F   77 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8121 (mtpt)
REVERT: F   93 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7707 (mt0)
REVERT: G   15 LYS cc_start: 0.7674 (mtpt) cc_final: 0.6939 (tttt)
REVERT: G   75 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8120 (mmtm)
REVERT: G   95 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8383 (tmtm)
  outliers start: 18
  outliers final: 8
  residues processed: 156
  average time/residue: 2.0125
  time to fit residues: 330.6122
Evaluate side-chains
  161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 88 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
D  44 GLN
E  68 GLN
E  76 GLN
H  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.174429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.133032 restraints weight = 10554.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.92
r_work: 0.3353 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12775  Z= 0.242
  Angle     :  0.627   7.718  18498  Z= 0.372
  Chirality :  0.037   0.146   2109
  Planarity :  0.005   0.043   1335
  Dihedral  : 30.932 175.597   4096
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.09 %
    Favored  : 80.22 %
  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:  2.51 (0.29), residues: 743
  helix:  2.26 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.16 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.013   0.002   TYR B  51 
 ARG   0.008   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06558 (  736)
  hydrogen bonds       : angle       3.09006 ( 1861)
  covalent geometry    : bond        0.00542 (12775)
  covalent geometry    : angle       0.62650 (18498)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8528 (pm20) cc_final: 0.8290 (pm20)
REVERT: A  131 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7550 (mtp180)
REVERT: B   52 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7711 (mp0)
REVERT: B   79 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8438 (mtmm)
REVERT: C   36 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8229 (mmpt)
REVERT: C   92 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8008 (mt-10)
REVERT: D   73 GLU cc_start: 0.8647 (tp30) cc_final: 0.8407 (tp30)
REVERT: E  115 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8253 (mppt)
REVERT: F   27 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8297 (mm110)
REVERT: F   77 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8170 (mtpt)
REVERT: F   93 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7813 (mt0)
REVERT: G   15 LYS cc_start: 0.7684 (mtpt) cc_final: 0.6985 (tttt)
REVERT: G   75 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8177 (mmtm)
REVERT: G   95 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8405 (tmtm)
  outliers start: 17
  outliers final: 8
  residues processed: 151
  average time/residue: 2.0079
  time to fit residues: 318.4373
Evaluate side-chains
  157 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain H residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
C 104 GLN
D  44 GLN
E  68 GLN
E  76 GLN
H  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.174574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.133151 restraints weight = 10581.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 0.92
r_work: 0.3355 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12775  Z= 0.227
  Angle     :  0.621   7.516  18498  Z= 0.370
  Chirality :  0.036   0.133   2109
  Planarity :  0.004   0.043   1335
  Dihedral  : 30.930 175.693   4096
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.41 %
    Favored  : 80.06 %
  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:  2.48 (0.29), residues: 743
  helix:  2.23 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.012   0.002   TYR E  54 
 ARG   0.008   0.001   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06511 (  736)
  hydrogen bonds       : angle       3.08811 ( 1861)
  covalent geometry    : bond        0.00507 (12775)
  covalent geometry    : angle       0.62128 (18498)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11777.01 seconds
wall clock time: 205 minutes 58.16 seconds (12358.16 seconds total)