Starting phenix.real_space_refine
on Wed Sep 17 21:31:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k43_62042/09_2025/9k43_62042.cif"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.052
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     289      5.49       5
     S      10      5.16       5
     C    6542      2.51       5
     N    2197      2.21       5
     O    2776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11814
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2985
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.79, per 1000 atoms: 0.24
  Number of scatterers: 11814
  At special positions: 0
  Unit cell: (118.992, 97.552, 114.704, 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      10     16.00
     P     289     15.00
     O    2776      8.00
     N    2197      7.00
     C    6542      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: 1.02
  Conformation dependent library (CDL) restraints added in 387.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      75.8% alpha, 2.7% beta
      143 base pairs and 244 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.601A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.944A  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 131
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.508A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    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 27 through 33
    Processing helix  chain 'C' and resid 37 through 49
    Processing helix  chain 'C' and resid 56 through 85
    Processing helix  chain 'C' and resid 91 through 102
      removed outlier: 3.572A  pdb=" N   ASP C 102 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 109
    Processing helix  chain 'C' and resid 123 through 127
      removed outlier: 3.560A  pdb=" N   ILE C 127 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 146
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.541A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.927A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    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: 3.661A  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
      removed outlier: 3.647A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 33
    Processing helix  chain 'G' and resid 37 through 49
    Processing helix  chain 'G' and resid 56 through 85
    Processing helix  chain 'G' and resid 91 through 102
      removed outlier: 3.573A  pdb=" N   ASP G 102 " --> pdb=" O   ALA G  98 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 109
    Processing helix  chain 'G' and resid 123 through 127
      removed outlier: 3.560A  pdb=" N   ILE G 127 " --> pdb=" O   LYS G 124 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.092A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55
      removed outlier: 7.031A  pdb=" N   ARG C  54 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113
      removed outlier: 6.451A  pdb=" N   THR C 112 " --> 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: 7.269A  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 54 through 55
      removed outlier: 6.753A  pdb=" N   ARG G  54 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90

    417 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      244 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 1.44 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: 2090
        1.33 -     1.45: 4235
        1.45 -     1.57: 5699
        1.57 -     1.69: 577
        1.69 -     1.81: 18
  Bond restraints: 12619
  Sorted by residual:
  bond pdb=" O3'  DG J  23 "
       pdb=" P    DC J  24 "
    ideal  model  delta    sigma   weight residual
    1.607  1.664 -0.057 1.50e-02 4.44e+03 1.45e+01
  bond pdb=" O3'  DT J  15 "
       pdb=" P    DA J  16 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.50e-02 4.44e+03 1.37e+01
  bond pdb=" O3'  DA J -15 "
       pdb=" P    DA J -14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.660 -0.053 1.50e-02 4.44e+03 1.25e+01
  bond pdb=" O3'  DA I -69 "
       pdb=" P    DG I -68 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.10e+01
  bond pdb=" O3'  DG J -69 "
       pdb=" P    DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.607  1.655 -0.048 1.50e-02 4.44e+03 1.04e+01
  ... (remaining 12614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17698
        1.60 -     3.19: 524
        3.19 -     4.79: 53
        4.79 -     6.39: 5
        6.39 -     7.98: 5
  Bond angle restraints: 18285
  Sorted by residual:
  angle pdb=" O3'  DG J   4 "
        pdb=" C3'  DG J   4 "
        pdb=" C2'  DG J   4 "
      ideal   model   delta    sigma   weight residual
     111.50  103.52    7.98 1.50e+00 4.44e-01 2.83e+01
  angle pdb=" N   ASN F  25 "
        pdb=" CA  ASN F  25 "
        pdb=" C   ASN F  25 "
      ideal   model   delta    sigma   weight residual
     113.15  107.42    5.73 1.19e+00 7.06e-01 2.32e+01
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  104.51    6.99 1.50e+00 4.44e-01 2.17e+01
  angle pdb=" N   GLY D 127 "
        pdb=" CA  GLY D 127 "
        pdb=" C   GLY D 127 "
      ideal   model   delta    sigma   weight residual
     111.02  118.02   -7.00 1.86e+00 2.89e-01 1.41e+01
  angle pdb=" N   GLY H 127 "
        pdb=" CA  GLY H 127 "
        pdb=" C   GLY H 127 "
      ideal   model   delta    sigma   weight residual
     110.77  117.84   -7.07 1.93e+00 2.68e-01 1.34e+01
  ... (remaining 18280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 4190
       17.37 -    34.75: 1117
       34.75 -    52.12: 1125
       52.12 -    69.49: 375
       69.49 -    86.87: 18
  Dihedral angle restraints: 6825
    sinusoidal: 4679
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CA  ASN F  64 "
           pdb=" CB  ASN F  64 "
           pdb=" CG  ASN F  64 "
           pdb=" OD1 ASN F  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -163.56   73.56     2      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CG  ARG F  39 "
           pdb=" CD  ARG F  39 "
           pdb=" NE  ARG F  39 "
           pdb=" CZ  ARG F  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.84  -43.84     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG C  54 "
           pdb=" CD  ARG C  54 "
           pdb=" NE  ARG C  54 "
           pdb=" CZ  ARG C  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.42  -43.58     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 6822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1803
       0.049 -    0.099: 242
       0.099 -    0.148: 42
       0.148 -    0.197: 8
       0.197 -    0.246: 2
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" C3'  DG J   4 "
            pdb=" C4'  DG J   4 "
            pdb=" O3'  DG J   4 "
            pdb=" C2'  DG J   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.91    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3'  DC J -26 "
            pdb=" C4'  DC J -26 "
            pdb=" O3'  DC J -26 "
            pdb=" C2'  DC J -26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C3'  DG I -71 "
            pdb=" C4'  DG I -71 "
            pdb=" O3'  DG I -71 "
            pdb=" C2'  DG I -71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 2094 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.48e+00
        pdb=" N   PRO D 126 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO E  43 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "    0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO B  32 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1806
        2.77 -     3.30: 10340
        3.30 -     3.83: 23767
        3.83 -     4.37: 27537
        4.37 -     4.90: 39377
  Nonbonded interactions: 102827
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  59 "
            pdb=" OE2 GLU B  63 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" NH2 ARG C  43 "
            pdb=" OE1 GLU D  58 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NH2 ARG G  43 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.328 3.120
  ... (remaining 102822 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'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
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=0.00 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:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.200
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
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   0.060  12619  Z= 0.204
  Angle     :  0.607   7.984  18285  Z= 0.380
  Chirality :  0.037   0.246   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 28.505  86.868   5437
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 24.60 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.81 (0.30), residues: 728
  helix:  2.61 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.51 (0.40), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  48 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.007   0.001   PHE B 100 
 HIS   0.007   0.001   HIS C 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (12619)
  covalent geometry    : angle       0.60731 (18285)
  hydrogen bonds       : bond        0.10775 (  785)
  hydrogen bonds       : angle       4.37290 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 177
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8627 (m-10) cc_final: 0.8137 (m-10)
REVERT: D  106 TYR cc_start: 0.8802 (m-10) cc_final: 0.8577 (m-10)
REVERT: H   85 MET cc_start: 0.8612 (mmm) cc_final: 0.8392 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 181
  average time/residue: 0.7693
  time to fit residues: 148.3960
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 128
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain F residue   96 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0030
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0670
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5930

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  75 HIS
B  93 GLN
** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
E  68 GLN
F  64 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.054182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.039664 restraints weight = 56918.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.13
r_work: 0.2806 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12619  Z= 0.152
  Angle     :  0.559   7.150  18285  Z= 0.339
  Chirality :  0.033   0.156   2097
  Planarity :  0.004   0.033   1296
  Dihedral  : 30.563  88.167   3979
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 27.33 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.26 (0.30), residues: 728
  helix:  2.90 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.32 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 122 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.019   0.001   PHE H  88 
 HIS   0.003   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12619)
  covalent geometry    : angle       0.55897 (18285)
  hydrogen bonds       : bond        0.03553 (  785)
  hydrogen bonds       : angle       2.82691 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.9245 (m-10) cc_final: 0.8413 (m-10)
REVERT: C   54 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7236 (mtp180)
REVERT: C   68 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8765 (tt0)
REVERT: C  102 ASP cc_start: 0.8820 (t0) cc_final: 0.8538 (t0)
REVERT: D  106 TYR cc_start: 0.9020 (m-10) cc_final: 0.8465 (m-10)
REVERT: D  136 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8959 (tp30)
REVERT: F   44 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8912 (mtpp)
REVERT: G  102 ASP cc_start: 0.8907 (t0) cc_final: 0.7960 (t0)
REVERT: G  110 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8670 (mmmm)
  outliers start: 17
  outliers final: 4
  residues processed: 167
  average time/residue: 0.7158
  time to fit residues: 128.1182
Evaluate side-chains
  141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain G residue   82 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
C 121 HIS
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.049608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.035260 restraints weight = 58172.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 2.29
r_work: 0.2679 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12619  Z= 0.240
  Angle     :  0.606   7.182  18285  Z= 0.362
  Chirality :  0.036   0.152   2097
  Planarity :  0.004   0.044   1296
  Dihedral  : 31.235  87.415   3978
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 27.65 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.24 (0.30), residues: 728
  helix:  2.92 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.47 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  89 
 TYR   0.026   0.002   TYR H 106 
 PHE   0.006   0.001   PHE C  36 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (12619)
  covalent geometry    : angle       0.60650 (18285)
  hydrogen bonds       : bond        0.04517 (  785)
  hydrogen bonds       : angle       3.08952 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9174 (mt-10)
REVERT: A   97 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8438 (mp0)
REVERT: C   54 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7250 (mtp180)
REVERT: C   68 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8844 (tt0)
REVERT: C  102 ASP cc_start: 0.8861 (t0) cc_final: 0.8554 (t0)
REVERT: D   56 ASN cc_start: 0.9479 (m-40) cc_final: 0.9137 (m-40)
REVERT: D  106 TYR cc_start: 0.9039 (m-10) cc_final: 0.8816 (m-10)
REVERT: D  136 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9051 (tp30)
REVERT: E   56 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9032 (tmmt)
REVERT: F   88 TYR cc_start: 0.9329 (m-10) cc_final: 0.8995 (m-10)
REVERT: G  102 ASP cc_start: 0.8731 (t0) cc_final: 0.8108 (t0)
REVERT: G  110 LYS cc_start: 0.9235 (mtmm) cc_final: 0.8868 (mmmm)
REVERT: H  116 GLU cc_start: 0.9323 (mp0) cc_final: 0.9094 (mp0)
REVERT: H  136 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9039 (tp30)
  outliers start: 25
  outliers final: 7
  residues processed: 145
  average time/residue: 0.7668
  time to fit residues: 118.6026
Evaluate side-chains
  134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    2.3788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.049181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.034698 restraints weight = 58083.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.26
r_work: 0.2671 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12619  Z= 0.214
  Angle     :  0.583   7.519  18285  Z= 0.351
  Chirality :  0.035   0.156   2097
  Planarity :  0.004   0.038   1296
  Dihedral  : 30.842  89.199   3977
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 29.90 %
    Favored  : 66.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.34 (0.30), residues: 728
  helix:  3.03 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.58 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C  40 
 TYR   0.028   0.002   TYR H 106 
 PHE   0.022   0.001   PHE D  88 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (12619)
  covalent geometry    : angle       0.58336 (18285)
  hydrogen bonds       : bond        0.03894 (  785)
  hydrogen bonds       : angle       2.91138 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (mp0)
REVERT: C   54 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7322 (mtp180)
REVERT: C  102 ASP cc_start: 0.8889 (t0) cc_final: 0.8603 (t0)
REVERT: D   56 ASN cc_start: 0.9494 (m-40) cc_final: 0.9209 (m-40)
REVERT: D   91 ASP cc_start: 0.9355 (t0) cc_final: 0.9005 (t0)
REVERT: D  136 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9060 (tp30)
REVERT: F   84 MET cc_start: 0.9280 (mmm) cc_final: 0.9077 (mmm)
REVERT: G  102 ASP cc_start: 0.8403 (t0) cc_final: 0.7774 (t0)
REVERT: G  106 ASP cc_start: 0.9352 (t0) cc_final: 0.9150 (t0)
REVERT: G  110 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8787 (mmmm)
REVERT: H   91 ASP cc_start: 0.9350 (t0) cc_final: 0.8995 (t0)
REVERT: H  116 GLU cc_start: 0.9318 (mp0) cc_final: 0.9028 (mp0)
REVERT: H  136 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9071 (tp30)
  outliers start: 21
  outliers final: 7
  residues processed: 147
  average time/residue: 0.7206
  time to fit residues: 113.4336
Evaluate side-chains
  136 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   82 SER
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 95 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.047018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033221 restraints weight = 58222.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.27
r_work: 0.2603 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  12619  Z= 0.303
  Angle     :  0.645   6.852  18285  Z= 0.381
  Chirality :  0.038   0.144   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 31.332  86.807   3977
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 29.90 %
    Favored  : 65.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.04 (0.31), residues: 728
  helix:  2.85 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.81 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  40 
 TYR   0.048   0.003   TYR H 106 
 PHE   0.006   0.001   PHE D  88 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 (12619)
  covalent geometry    : angle       0.64464 (18285)
  hydrogen bonds       : bond        0.04803 (  785)
  hydrogen bonds       : angle       3.22030 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8792 (mmm) cc_final: 0.8214 (mtm)
REVERT: C   54 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7214 (mtp180)
REVERT: C   68 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8856 (tt0)
REVERT: C  102 ASP cc_start: 0.8870 (t0) cc_final: 0.8587 (t0)
REVERT: D  136 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9064 (tp30)
REVERT: E   56 LYS cc_start: 0.9308 (ttpp) cc_final: 0.9057 (tmmt)
REVERT: E  120 MET cc_start: 0.8880 (mmm) cc_final: 0.8319 (mtm)
REVERT: F   84 MET cc_start: 0.9256 (mmm) cc_final: 0.8914 (mmm)
REVERT: G   30 SER cc_start: 0.9748 (OUTLIER) cc_final: 0.9448 (p)
REVERT: G   86 LYS cc_start: 0.9518 (mmmt) cc_final: 0.9300 (mmmm)
REVERT: G  102 ASP cc_start: 0.8460 (t0) cc_final: 0.7974 (t0)
REVERT: G  106 ASP cc_start: 0.9406 (t0) cc_final: 0.9135 (t0)
REVERT: G  110 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8905 (mmmm)
REVERT: H  116 GLU cc_start: 0.9340 (mp0) cc_final: 0.9090 (mp0)
  outliers start: 27
  outliers final: 10
  residues processed: 144
  average time/residue: 0.7162
  time to fit residues: 110.4806
Evaluate side-chains
  134 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.048855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.035176 restraints weight = 56958.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 2.25
r_work: 0.2686 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12619  Z= 0.156
  Angle     :  0.582   7.302  18285  Z= 0.350
  Chirality :  0.034   0.158   2097
  Planarity :  0.004   0.039   1296
  Dihedral  : 30.705  89.180   3977
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 32.48 %
    Favored  : 64.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.31), residues: 728
  helix:  2.98 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.69 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  40 
 TYR   0.036   0.002   TYR H 106 
 PHE   0.024   0.001   PHE D  88 
 HIS   0.003   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12619)
  covalent geometry    : angle       0.58248 (18285)
  hydrogen bonds       : bond        0.03520 (  785)
  hydrogen bonds       : angle       2.77900 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.9120 (m-10) cc_final: 0.8817 (m-10)
REVERT: C   46 LYS cc_start: 0.9129 (mttm) cc_final: 0.8722 (mmtt)
REVERT: C   54 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7294 (mtp180)
REVERT: C   68 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8782 (tt0)
REVERT: C  102 ASP cc_start: 0.8877 (t0) cc_final: 0.8587 (t0)
REVERT: D   91 ASP cc_start: 0.9331 (t0) cc_final: 0.9002 (t0)
REVERT: D   98 GLN cc_start: 0.9274 (tp40) cc_final: 0.9003 (tp40)
REVERT: D  128 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8170 (tm-30)
REVERT: D  136 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8917 (tp30)
REVERT: E   56 LYS cc_start: 0.9267 (ttpp) cc_final: 0.8958 (tmmt)
REVERT: G   30 SER cc_start: 0.9757 (OUTLIER) cc_final: 0.9491 (p)
REVERT: G   54 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7319 (mtp180)
REVERT: G  102 ASP cc_start: 0.8359 (t0) cc_final: 0.7853 (t0)
REVERT: G  106 ASP cc_start: 0.9291 (t0) cc_final: 0.9022 (t0)
REVERT: G  109 ILE cc_start: 0.8898 (mt) cc_final: 0.8666 (mt)
REVERT: G  110 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8732 (mmmm)
REVERT: H   91 ASP cc_start: 0.9348 (t0) cc_final: 0.9023 (t0)
REVERT: H   98 GLN cc_start: 0.9131 (tp40) cc_final: 0.8891 (tp-100)
REVERT: H  116 GLU cc_start: 0.9323 (mp0) cc_final: 0.8979 (mp0)
REVERT: H  136 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.9058 (tp30)
  outliers start: 18
  outliers final: 4
  residues processed: 152
  average time/residue: 0.7088
  time to fit residues: 115.5256
Evaluate side-chains
  141 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   54 ARG
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  98 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.046666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.032494 restraints weight = 57498.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 2.26
r_work: 0.2598 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8911
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  12619  Z= 0.305
  Angle     :  0.659   9.973  18285  Z= 0.387
  Chirality :  0.037   0.146   2097
  Planarity :  0.004   0.042   1296
  Dihedral  : 31.218  88.196   3977
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 33.76 %
    Favored  : 63.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.10 (0.31), residues: 728
  helix:  2.86 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.67 (0.42), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  92 
 TYR   0.052   0.003   TYR D 106 
 PHE   0.022   0.001   PHE H  88 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 (12619)
  covalent geometry    : angle       0.65882 (18285)
  hydrogen bonds       : bond        0.04653 (  785)
  hydrogen bonds       : angle       3.17959 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8766 (mmm) cc_final: 0.8083 (mtm)
REVERT: C   54 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7206 (mtp180)
REVERT: C   68 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8864 (tt0)
REVERT: C  102 ASP cc_start: 0.8862 (t0) cc_final: 0.8567 (t0)
REVERT: D   91 ASP cc_start: 0.9402 (t0) cc_final: 0.9051 (t0)
REVERT: D  136 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9072 (tp30)
REVERT: E   56 LYS cc_start: 0.9271 (ttpp) cc_final: 0.8965 (tmmt)
REVERT: E  120 MET cc_start: 0.8817 (mmm) cc_final: 0.8219 (mtm)
REVERT: G   30 SER cc_start: 0.9748 (OUTLIER) cc_final: 0.9444 (p)
REVERT: G   86 LYS cc_start: 0.9526 (mmmt) cc_final: 0.9313 (mmmm)
REVERT: G  102 ASP cc_start: 0.8497 (t0) cc_final: 0.8093 (t0)
REVERT: G  106 ASP cc_start: 0.9382 (t0) cc_final: 0.9126 (t0)
REVERT: G  110 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8835 (mmmm)
REVERT: H   91 ASP cc_start: 0.9410 (t0) cc_final: 0.9077 (t0)
REVERT: H  116 GLU cc_start: 0.9350 (mp0) cc_final: 0.9030 (mp0)
REVERT: H  136 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9110 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 132
  average time/residue: 0.7719
  time to fit residues: 108.8960
Evaluate side-chains
  132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue   66 ILE
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
H  98 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.047893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.033937 restraints weight = 57385.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.26
r_work: 0.2653 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12619  Z= 0.181
  Angle     :  0.606   8.533  18285  Z= 0.361
  Chirality :  0.034   0.148   2097
  Planarity :  0.004   0.038   1296
  Dihedral  : 30.783  89.894   3977
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 34.24 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.20 (0.31), residues: 728
  helix:  2.92 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.59 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  92 
 TYR   0.059   0.003   TYR D 106 
 PHE   0.027   0.001   PHE D  88 
 HIS   0.004   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (12619)
  covalent geometry    : angle       0.60648 (18285)
  hydrogen bonds       : bond        0.03795 (  785)
  hydrogen bonds       : angle       2.88294 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.9112 (m-10) cc_final: 0.8795 (m-10)
REVERT: C   54 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7267 (mtp180)
REVERT: C   68 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8818 (tt0)
REVERT: C  102 ASP cc_start: 0.8861 (t0) cc_final: 0.8589 (t0)
REVERT: D   91 ASP cc_start: 0.9360 (t0) cc_final: 0.9029 (t0)
REVERT: D  128 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8242 (tm-30)
REVERT: D  136 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8942 (tp30)
REVERT: E   56 LYS cc_start: 0.9307 (ttpp) cc_final: 0.8974 (tmmt)
REVERT: G   30 SER cc_start: 0.9755 (OUTLIER) cc_final: 0.9483 (p)
REVERT: G   86 LYS cc_start: 0.9500 (mmmt) cc_final: 0.9231 (mmmm)
REVERT: G  102 ASP cc_start: 0.8326 (t0) cc_final: 0.7876 (t0)
REVERT: G  106 ASP cc_start: 0.9299 (t0) cc_final: 0.9033 (t0)
REVERT: G  109 ILE cc_start: 0.9005 (mt) cc_final: 0.8745 (mt)
REVERT: G  110 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8747 (mmmm)
REVERT: H   91 ASP cc_start: 0.9366 (t0) cc_final: 0.9030 (t0)
REVERT: H   98 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8982 (tp40)
REVERT: H  116 GLU cc_start: 0.9341 (mp0) cc_final: 0.8996 (mp0)
REVERT: H  136 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9061 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 143
  average time/residue: 0.7156
  time to fit residues: 109.8382
Evaluate side-chains
  142 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue   98 GLN
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 93 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.048621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.034705 restraints weight = 57084.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 2.28
r_work: 0.2678 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12619  Z= 0.163
  Angle     :  0.610  11.041  18285  Z= 0.360
  Chirality :  0.034   0.151   2097
  Planarity :  0.004   0.036   1296
  Dihedral  : 30.686  89.618   3977
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 34.08 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.17 (0.31), residues: 728
  helix:  2.87 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.51 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  92 
 TYR   0.045   0.002   TYR B  88 
 PHE   0.022   0.001   PHE H  88 
 HIS   0.004   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12619)
  covalent geometry    : angle       0.61008 (18285)
  hydrogen bonds       : bond        0.03528 (  785)
  hydrogen bonds       : angle       2.81771 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   54 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7245 (mtp180)
REVERT: C   68 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8814 (tt0)
REVERT: C  102 ASP cc_start: 0.8878 (t0) cc_final: 0.8592 (t0)
REVERT: D   91 ASP cc_start: 0.9344 (t0) cc_final: 0.9023 (t0)
REVERT: D   98 GLN cc_start: 0.9266 (tp40) cc_final: 0.9047 (tp40)
REVERT: D  128 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8177 (tm-30)
REVERT: D  136 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8944 (tp30)
REVERT: E   56 LYS cc_start: 0.9307 (ttpp) cc_final: 0.8966 (tmmt)
REVERT: G   30 SER cc_start: 0.9754 (OUTLIER) cc_final: 0.9489 (p)
REVERT: G   86 LYS cc_start: 0.9485 (mmmt) cc_final: 0.9215 (mmmm)
REVERT: G  102 ASP cc_start: 0.8352 (t0) cc_final: 0.7882 (t0)
REVERT: G  106 ASP cc_start: 0.9266 (t0) cc_final: 0.8973 (t0)
REVERT: G  109 ILE cc_start: 0.8879 (mt) cc_final: 0.8615 (mt)
REVERT: G  110 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8674 (mmmm)
REVERT: H   91 ASP cc_start: 0.9373 (t0) cc_final: 0.9051 (t0)
REVERT: H  116 GLU cc_start: 0.9324 (mp0) cc_final: 0.8879 (mp0)
REVERT: H  136 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.9061 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 146
  average time/residue: 0.7122
  time to fit residues: 111.5504
Evaluate side-chains
  144 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.046800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.032664 restraints weight = 58043.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 2.29
r_work: 0.2608 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  12619  Z= 0.287
  Angle     :  0.665  11.448  18285  Z= 0.388
  Chirality :  0.037   0.140   2097
  Planarity :  0.004   0.034   1296
  Dihedral  : 31.109  87.828   3977
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 34.57 %
    Favored  : 63.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.31), residues: 728
  helix:  2.65 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.65 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  92 
 TYR   0.067   0.004   TYR H 106 
 PHE   0.027   0.001   PHE D  88 
 HIS   0.004   0.001   HIS D 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00647 (12619)
  covalent geometry    : angle       0.66500 (18285)
  hydrogen bonds       : bond        0.04626 (  785)
  hydrogen bonds       : angle       3.21548 ( 1969)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   54 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7249 (mtp180)
REVERT: C   68 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8871 (tt0)
REVERT: C  102 ASP cc_start: 0.8872 (t0) cc_final: 0.8574 (t0)
REVERT: D   91 ASP cc_start: 0.9423 (t0) cc_final: 0.9085 (t0)
REVERT: D  136 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8965 (tp30)
REVERT: E   56 LYS cc_start: 0.9303 (ttpp) cc_final: 0.8965 (tmmt)
REVERT: E  120 MET cc_start: 0.8838 (mmm) cc_final: 0.8144 (mtm)
REVERT: G   30 SER cc_start: 0.9754 (OUTLIER) cc_final: 0.9454 (p)
REVERT: G   86 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9271 (mmmm)
REVERT: G  102 ASP cc_start: 0.8484 (t0) cc_final: 0.7975 (t0)
REVERT: G  106 ASP cc_start: 0.9359 (t0) cc_final: 0.9090 (t0)
REVERT: G  110 LYS cc_start: 0.9240 (mtmm) cc_final: 0.8819 (mmmm)
REVERT: H   91 ASP cc_start: 0.9424 (t0) cc_final: 0.9085 (t0)
REVERT: H  116 GLU cc_start: 0.9363 (mp0) cc_final: 0.9050 (mp0)
REVERT: H  136 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9070 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 132
  average time/residue: 0.7667
  time to fit residues: 108.1278
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   27 THR
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   54 ARG
Chi-restraints excluded: chain C residue   68 GLU
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   27 THR
Chi-restraints excluded: chain G residue   30 SER
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  98 GLN
** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.048485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.034835 restraints weight = 57603.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.28
r_work: 0.2677 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12619  Z= 0.167
  Angle     :  0.622  11.370  18285  Z= 0.366
  Chirality :  0.034   0.152   2097
  Planarity :  0.004   0.037   1296
  Dihedral  : 30.629  89.176   3977
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 35.21 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.95 (0.31), residues: 728
  helix:  2.71 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.57 (0.43), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  92 
 TYR   0.040   0.002   TYR B  88 
 PHE   0.028   0.001   PHE H  88 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12619)
  covalent geometry    : angle       0.62185 (18285)
  hydrogen bonds       : bond        0.03625 (  785)
  hydrogen bonds       : angle       2.90532 ( 1969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4018.05 seconds
wall clock time: 69 minutes 22.08 seconds (4162.08 seconds total)