Starting phenix.real_space_refine
on Wed Sep 17 21:35:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2025/9k41_62038.cif"
  }
  resolution = 2.81
  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      14      5.16       5
     C    6585      2.51       5
     N    2168      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 11828
  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: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    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: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    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: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.77, per 1000 atoms: 0.23
  Number of scatterers: 11828
  At special positions: 0
  Unit cell: (121.136, 75.04, 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      14     16.00
     P     289     15.00
     O    2772      8.00
     N    2168      7.00
     C    6585      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: 0.93
  Conformation dependent library (CDL) restraints added in 359.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 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:
      33 helices and 10 sheets defined
      72.3% alpha, 3.2% beta
      145 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.559A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.644A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 31
      removed outlier: 3.546A  pdb=" N   ALA C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    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 127 through 147
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.687A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.598A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 98
    Processing helix  chain 'G' and resid 99 through 106
    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
      removed outlier: 3.528A  pdb=" N   ALA H 130 " --> pdb=" O   PRO H 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.044A  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: 6.439A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.447A  pdb=" N   ARG C  51 " --> 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 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.111A  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 51 through 52
      removed outlier: 7.241A  pdb=" N   ARG G  51 " --> 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 86 through 87

    405 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 1.29 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: 2177
        1.33 -     1.45: 4095
        1.45 -     1.57: 5758
        1.57 -     1.69: 577
        1.69 -     1.81: 26
  Bond restraints: 12633
  Sorted by residual:
  bond pdb=" O3'  DC J -26 "
       pdb=" P    DA J -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.50e-02 4.44e+03 9.38e+00
  bond pdb=" O3'  DA I  -9 "
       pdb=" P    DA I  -8 "
    ideal  model  delta    sigma   weight residual
    1.607  1.642 -0.035 1.50e-02 4.44e+03 5.56e+00
  bond pdb=" O3'  DC I  -6 "
       pdb=" P    DA I  -5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.640 -0.033 1.50e-02 4.44e+03 4.78e+00
  bond pdb=" CA  ILE F  26 "
       pdb=" CB  ILE F  26 "
    ideal  model  delta    sigma   weight residual
    1.538  1.553 -0.015 1.37e-02 5.33e+03 1.25e+00
  bond pdb=" N   ASP B  24 "
       pdb=" CA  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.014 1.29e-02 6.01e+03 1.22e+00
  ... (remaining 12628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 17094
        1.03 -     2.07: 911
        2.07 -     3.10: 261
        3.10 -     4.13: 20
        4.13 -     5.17: 13
  Bond angle restraints: 18299
  Sorted by residual:
  angle pdb=" N   ASN B  25 "
        pdb=" CA  ASN B  25 "
        pdb=" C   ASN B  25 "
      ideal   model   delta    sigma   weight residual
     113.20  109.14    4.06 1.21e+00 6.83e-01 1.12e+01
  angle pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
        pdb=" C   ASP F  24 "
      ideal   model   delta    sigma   weight residual
     111.17  115.78   -4.61 1.41e+00 5.03e-01 1.07e+01
  angle pdb=" O3'  DG J -27 "
        pdb=" C3'  DG J -27 "
        pdb=" C2'  DG J -27 "
      ideal   model   delta    sigma   weight residual
     111.50  106.84    4.66 1.50e+00 4.44e-01 9.67e+00
  angle pdb=" O3'  DA I  -8 "
        pdb=" C3'  DA I  -8 "
        pdb=" C2'  DA I  -8 "
      ideal   model   delta    sigma   weight residual
     111.50  106.95    4.55 1.50e+00 4.44e-01 9.22e+00
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  107.12    4.38 1.50e+00 4.44e-01 8.52e+00
  ... (remaining 18294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.84: 4451
       20.84 -    41.69: 1347
       41.69 -    62.53: 1084
       62.53 -    83.38: 50
       83.38 -   104.22: 3
  Dihedral angle restraints: 6935
    sinusoidal: 4785
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.93   16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CG  ARG A  49 "
           pdb=" CD  ARG A  49 "
           pdb=" NE  ARG A  49 "
           pdb=" CZ  ARG A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.97  -42.97     2      1.50e+01 4.44e-03 9.91e+00
  dihedral pdb=" C4'  DG J -17 "
           pdb=" C3'  DG J -17 "
           pdb=" O3'  DG J -17 "
           pdb=" P    DC J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -35.78 -104.22     1      3.50e+01 8.16e-04 9.76e+00
  ... (remaining 6932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1640
       0.040 -    0.079: 364
       0.079 -    0.119: 68
       0.119 -    0.158: 11
       0.158 -    0.198: 4
  Chirality restraints: 2087
  Sorted by residual:
  chirality pdb=" C3'  DA I  -8 "
            pdb=" C4'  DA I  -8 "
            pdb=" O3'  DA I  -8 "
            pdb=" C2'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" C3'  DG J -27 "
            pdb=" C4'  DG J -27 "
            pdb=" O3'  DG J -27 "
            pdb=" C2'  DG J -27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 8.99e-01
  ... (remaining 2084 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO H 126 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  44 "    0.011 2.00e-02 2.50e+03   1.07e-02 2.60e+00
        pdb=" N1   DC J  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  44 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DC J  44 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC J  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  44 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC J  44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  44 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.29e+00
        pdb=" N   PRO D 126 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1308
        2.75 -     3.29: 10382
        3.29 -     3.82: 23519
        3.82 -     4.36: 27964
        4.36 -     4.90: 39816
  Nonbonded interactions: 102989
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  55 "
            pdb=" OP1  DT I -46 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH2 ARG G  41 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   SER G  85 "
            pdb=" OG  SER G  85 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.309 3.120
  ... (remaining 102984 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:             1.150
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.730
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
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   0.046  12633  Z= 0.179
  Angle     :  0.561   5.167  18299  Z= 0.350
  Chirality :  0.036   0.198   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 28.881 104.221   5547
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 22.99 %
    Favored  : 75.72 %
  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:  1.93 (0.30), residues: 730
  helix:  1.71 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.010   0.002   TYR B  98 
 PHE   0.006   0.001   PHE C  34 
 HIS   0.002   0.000   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12633)
  covalent geometry    : angle       0.56064 (18299)
  hydrogen bonds       : bond        0.12474 (  753)
  hydrogen bonds       : angle       4.65008 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.312 
Fit side-chains
REVERT: C   81 ASP cc_start: 0.8800 (m-30) cc_final: 0.8594 (m-30)
REVERT: C   99 ASP cc_start: 0.8819 (t70) cc_final: 0.7685 (t0)
REVERT: C  121 ASN cc_start: 0.9301 (t0) cc_final: 0.8789 (t0)
REVERT: D   82 MET cc_start: 0.9307 (tpt) cc_final: 0.9096 (mmm)
REVERT: D   91 ASP cc_start: 0.9111 (t70) cc_final: 0.8801 (t0)
REVERT: G   81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8775 (m-30)
REVERT: G   99 ASP cc_start: 0.8900 (t70) cc_final: 0.8635 (t0)
REVERT: G  121 ASN cc_start: 0.9264 (t0) cc_final: 0.8854 (t0)
REVERT: H   58 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: H   91 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0)
REVERT: H  128 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8131 (tm-30)
  outliers start: 8
  outliers final: 0
  residues processed: 148
  average time/residue: 0.8858
  time to fit residues: 138.2749
Evaluate side-chains
  110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
A 113 HIS
B  25 ASN
B  27 GLN
B  75 HIS
C  33 GLN
C  82 ASN
D  56 ASN
E  68 GLN
E 108 ASN
E 113 HIS
F  75 HIS
G  33 GLN
G  77 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.052772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.036675 restraints weight = 53067.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 1.92
r_work: 0.2698 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  12633  Z= 0.205
  Angle     :  0.583   7.031  18299  Z= 0.352
  Chirality :  0.034   0.123   2087
  Planarity :  0.004   0.039   1304
  Dihedral  : 31.237  99.030   4071
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 23.15 %
    Favored  : 75.24 %
  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:  2.88 (0.31), residues: 730
  helix:  2.50 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.06 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H 105 
 TYR   0.010   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.004   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (12633)
  covalent geometry    : angle       0.58264 (18299)
  hydrogen bonds       : bond        0.04611 (  753)
  hydrogen bonds       : angle       2.84482 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: B   50 ILE cc_start: 0.9458 (mm) cc_final: 0.9210 (mp)
REVERT: C   81 ASP cc_start: 0.9060 (m-30) cc_final: 0.8824 (m-30)
REVERT: C   99 ASP cc_start: 0.8777 (t70) cc_final: 0.7771 (t0)
REVERT: C  101 GLU cc_start: 0.8331 (pm20) cc_final: 0.7685 (pm20)
REVERT: C  121 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8731 (t0)
REVERT: D   82 MET cc_start: 0.9449 (tpt) cc_final: 0.9151 (mmm)
REVERT: D   91 ASP cc_start: 0.9370 (t70) cc_final: 0.8996 (t0)
REVERT: D   94 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: D  128 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8353 (tp30)
REVERT: G   81 ASP cc_start: 0.9202 (m-30) cc_final: 0.8946 (m-30)
REVERT: G   99 ASP cc_start: 0.9197 (t70) cc_final: 0.8712 (t0)
REVERT: G  121 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8709 (t0)
REVERT: H   58 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: H   91 ASP cc_start: 0.9301 (t0) cc_final: 0.8931 (t0)
REVERT: H   94 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8436 (tp30)
REVERT: H  128 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8364 (tm-30)
  outliers start: 10
  outliers final: 3
  residues processed: 133
  average time/residue: 0.8191
  time to fit residues: 115.2993
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.052842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.036712 restraints weight = 53512.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.93
r_work: 0.2707 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  12633  Z= 0.167
  Angle     :  0.559   7.650  18299  Z= 0.339
  Chirality :  0.033   0.121   2087
  Planarity :  0.004   0.038   1304
  Dihedral  : 31.137  95.610   4071
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.19 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.27 (0.31), residues: 730
  helix:  2.78 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.08 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.006   0.001   PHE C  34 
 HIS   0.002   0.000   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12633)
  covalent geometry    : angle       0.55899 (18299)
  hydrogen bonds       : bond        0.03873 (  753)
  hydrogen bonds       : angle       2.62793 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 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: 14
    poor density    : 124
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: C   81 ASP cc_start: 0.9117 (m-30) cc_final: 0.8904 (m-30)
REVERT: C   99 ASP cc_start: 0.8733 (t70) cc_final: 0.7911 (t70)
REVERT: C  101 GLU cc_start: 0.8229 (pm20) cc_final: 0.7517 (pm20)
REVERT: C  121 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8680 (t0)
REVERT: D   82 MET cc_start: 0.9498 (tpt) cc_final: 0.9136 (mmm)
REVERT: D   91 ASP cc_start: 0.9369 (t70) cc_final: 0.8999 (t0)
REVERT: D   94 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: D  106 TYR cc_start: 0.8812 (m-10) cc_final: 0.8397 (m-80)
REVERT: D  128 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8387 (tp30)
REVERT: F   92 ARG cc_start: 0.9449 (OUTLIER) cc_final: 0.9075 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9166 (m-30) cc_final: 0.8934 (m-30)
REVERT: G   84 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8804 (mmmm)
REVERT: G   99 ASP cc_start: 0.9206 (t70) cc_final: 0.8656 (t0)
REVERT: G  121 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: H   58 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8285 (mm-30)
REVERT: H   91 ASP cc_start: 0.9312 (t0) cc_final: 0.8939 (t0)
REVERT: H   94 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8485 (tm-30)
REVERT: H  128 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8376 (tm-30)
  outliers start: 14
  outliers final: 5
  residues processed: 135
  average time/residue: 0.9099
  time to fit residues: 129.5091
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue   84 LYS
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0170
   chunk 85 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    3.6026

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D 107 ASN
E  39 HIS
G  82 ASN
H 107 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.049521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.033800 restraints weight = 53943.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.2767 rms_B_bonded: 1.95
r_work: 0.2599 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  12633  Z= 0.289
  Angle     :  0.641   9.543  18299  Z= 0.378
  Chirality :  0.037   0.129   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.951  96.821   4071
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.31 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.03 (0.31), residues: 730
  helix:  2.62 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.03 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 105 
 TYR   0.011   0.002   TYR H  63 
 PHE   0.007   0.001   PHE D  65 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 (12633)
  covalent geometry    : angle       0.64149 (18299)
  hydrogen bonds       : bond        0.05645 (  753)
  hydrogen bonds       : angle       3.01392 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9270 (mtpp)
REVERT: C   99 ASP cc_start: 0.8978 (t70) cc_final: 0.7890 (t0)
REVERT: C  101 GLU cc_start: 0.8307 (pm20) cc_final: 0.7590 (pm20)
REVERT: C  121 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8770 (t0)
REVERT: D   82 MET cc_start: 0.9507 (tpt) cc_final: 0.9265 (mmm)
REVERT: D   91 ASP cc_start: 0.9396 (t70) cc_final: 0.9062 (t0)
REVERT: D   94 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8719 (tm-30)
REVERT: D  106 TYR cc_start: 0.8835 (m-10) cc_final: 0.8437 (m-80)
REVERT: D  128 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8451 (tp30)
REVERT: E   80 THR cc_start: 0.9625 (m) cc_final: 0.9388 (m)
REVERT: G   82 ASN cc_start: 0.9213 (t0) cc_final: 0.8901 (t0)
REVERT: G   99 ASP cc_start: 0.9256 (t70) cc_final: 0.8818 (t0)
REVERT: G  121 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8686 (t0)
REVERT: H   58 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8437 (mm-30)
REVERT: H   91 ASP cc_start: 0.9336 (t0) cc_final: 0.8982 (t0)
REVERT: H   94 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8548 (tm-30)
REVERT: H  128 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8412 (tm-30)
  outliers start: 16
  outliers final: 5
  residues processed: 128
  average time/residue: 0.8546
  time to fit residues: 115.6050
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  56 ASN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.049948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.033827 restraints weight = 53737.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 1.95
r_work: 0.2618 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12633  Z= 0.225
  Angle     :  0.605   9.971  18299  Z= 0.360
  Chirality :  0.035   0.124   2087
  Planarity :  0.004   0.037   1304
  Dihedral  : 31.625  96.807   4071
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 23.31 %
    Favored  : 74.92 %
  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:  3.16 (0.31), residues: 730
  helix:  2.72 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.05 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 105 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.006   0.001   PHE C  34 
 HIS   0.003   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (12633)
  covalent geometry    : angle       0.60458 (18299)
  hydrogen bonds       : bond        0.04600 (  753)
  hydrogen bonds       : angle       2.76683 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.9376 (t0) cc_final: 0.9128 (t0)
REVERT: C   99 ASP cc_start: 0.8857 (t70) cc_final: 0.7823 (t0)
REVERT: C  101 GLU cc_start: 0.8256 (pm20) cc_final: 0.7761 (pm20)
REVERT: C  121 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8744 (t0)
REVERT: D   82 MET cc_start: 0.9549 (tpt) cc_final: 0.9198 (mmm)
REVERT: D   91 ASP cc_start: 0.9381 (t70) cc_final: 0.9041 (t0)
REVERT: D   94 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: D  128 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8446 (tp30)
REVERT: E   80 THR cc_start: 0.9635 (m) cc_final: 0.9410 (m)
REVERT: F   92 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.8942 (mtp-110)
REVERT: G   99 ASP cc_start: 0.9255 (t70) cc_final: 0.8782 (t0)
REVERT: G  121 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8703 (t0)
REVERT: H   58 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8495 (mm-30)
REVERT: H   91 ASP cc_start: 0.9334 (t0) cc_final: 0.8979 (t0)
REVERT: H   94 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8555 (tm-30)
REVERT: H  106 TYR cc_start: 0.8795 (m-10) cc_final: 0.8399 (m-10)
REVERT: H  128 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8409 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 123
  average time/residue: 0.8173
  time to fit residues: 106.1250
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 90 optimal weight:    6.9990
   chunk 68 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.050713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.034601 restraints weight = 53663.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 1.97
r_work: 0.2652 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12633  Z= 0.180
  Angle     :  0.585   9.663  18299  Z= 0.349
  Chirality :  0.033   0.121   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.332  95.335   4071
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 24.12 %
    Favored  : 73.95 %
  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:  3.30 (0.31), residues: 730
  helix:  2.83 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.02 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  49 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (12633)
  covalent geometry    : angle       0.58496 (18299)
  hydrogen bonds       : bond        0.03950 (  753)
  hydrogen bonds       : angle       2.61423 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.379 
Fit side-chains
REVERT: C   82 ASN cc_start: 0.9344 (t0) cc_final: 0.9132 (t0)
REVERT: C   99 ASP cc_start: 0.8854 (t70) cc_final: 0.7802 (t0)
REVERT: C  101 GLU cc_start: 0.8240 (pm20) cc_final: 0.7773 (pm20)
REVERT: C  121 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8731 (t0)
REVERT: D   82 MET cc_start: 0.9541 (tpt) cc_final: 0.9331 (mmm)
REVERT: D   91 ASP cc_start: 0.9387 (t70) cc_final: 0.9037 (t0)
REVERT: D   94 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: D  106 TYR cc_start: 0.8805 (m-10) cc_final: 0.8420 (m-80)
REVERT: D  128 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8399 (tp30)
REVERT: E   80 THR cc_start: 0.9584 (m) cc_final: 0.9379 (m)
REVERT: E  122 LYS cc_start: 0.9212 (ptpp) cc_final: 0.8988 (ptmm)
REVERT: G   99 ASP cc_start: 0.9223 (t70) cc_final: 0.8702 (t0)
REVERT: G  121 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8676 (t0)
REVERT: H   58 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: H   91 ASP cc_start: 0.9315 (t0) cc_final: 0.8936 (t0)
REVERT: H   94 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8528 (tm-30)
REVERT: H  106 TYR cc_start: 0.8743 (m-10) cc_final: 0.8399 (m-80)
REVERT: H  128 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8387 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 129
  average time/residue: 0.8127
  time to fit residues: 110.7966
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
G  82 ASN

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 = 0.049249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.033145 restraints weight = 53628.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 1.94
r_work: 0.2598 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8908
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  12633  Z= 0.264
  Angle     :  0.640  11.010  18299  Z= 0.373
  Chirality :  0.036   0.152   2087
  Planarity :  0.004   0.035   1304
  Dihedral  : 31.778  95.555   4071
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 25.24 %
    Favored  : 72.99 %
  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:  3.15 (0.31), residues: 730
  helix:  2.74 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.14 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  92 
 TYR   0.011   0.002   TYR B  88 
 PHE   0.010   0.001   PHE E  78 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 (12633)
  covalent geometry    : angle       0.63993 (18299)
  hydrogen bonds       : bond        0.05073 (  753)
  hydrogen bonds       : angle       2.87758 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.254 
Fit side-chains
REVERT: C   82 ASN cc_start: 0.9359 (t0) cc_final: 0.9134 (t0)
REVERT: C   99 ASP cc_start: 0.8929 (t70) cc_final: 0.7872 (t0)
REVERT: C  101 GLU cc_start: 0.8272 (pm20) cc_final: 0.7773 (pm20)
REVERT: C  121 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.8769 (t0)
REVERT: D   91 ASP cc_start: 0.9380 (t70) cc_final: 0.9046 (t0)
REVERT: D   94 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8746 (tm-30)
REVERT: D  106 TYR cc_start: 0.8856 (m-10) cc_final: 0.8369 (m-80)
REVERT: D  128 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8427 (tp30)
REVERT: G   28 MET cc_start: 0.9158 (ptt) cc_final: 0.8954 (ppp)
REVERT: G   99 ASP cc_start: 0.9259 (t70) cc_final: 0.8767 (t0)
REVERT: G  121 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8705 (t0)
REVERT: H   58 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8500 (mm-30)
REVERT: H   91 ASP cc_start: 0.9335 (t0) cc_final: 0.8976 (t0)
REVERT: H   94 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8558 (tm-30)
REVERT: H  106 TYR cc_start: 0.8829 (m-10) cc_final: 0.8378 (m-10)
REVERT: H  128 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8445 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 123
  average time/residue: 0.8256
  time to fit residues: 107.4768
Evaluate side-chains
  118 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  121 ASN
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
G  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.049643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.033715 restraints weight = 53736.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 1.91
r_work: 0.2616 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12633  Z= 0.213
  Angle     :  0.625  11.938  18299  Z= 0.365
  Chirality :  0.035   0.135   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.513  95.574   4071
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.92 %
    Favored  : 72.99 %
  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 (0.31), residues: 730
  helix:  2.81 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.12 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  80 
 TYR   0.012   0.001   TYR B  88 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (12633)
  covalent geometry    : angle       0.62465 (18299)
  hydrogen bonds       : bond        0.04372 (  753)
  hydrogen bonds       : angle       2.71912 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.9328 (t0) cc_final: 0.9124 (t0)
REVERT: C   99 ASP cc_start: 0.8876 (t70) cc_final: 0.7837 (t0)
REVERT: C  101 GLU cc_start: 0.8233 (pm20) cc_final: 0.7821 (pm20)
REVERT: C  121 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8768 (t0)
REVERT: D   91 ASP cc_start: 0.9349 (t0) cc_final: 0.9012 (t0)
REVERT: D   94 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: D  128 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8452 (tp30)
REVERT: F   88 TYR cc_start: 0.9317 (m-10) cc_final: 0.8058 (m-10)
REVERT: G   99 ASP cc_start: 0.9233 (t70) cc_final: 0.8795 (t0)
REVERT: G  121 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8695 (t0)
REVERT: H   58 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8532 (mm-30)
REVERT: H   91 ASP cc_start: 0.9321 (t0) cc_final: 0.8951 (t0)
REVERT: H   94 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8560 (tm-30)
REVERT: H  106 TYR cc_start: 0.8777 (m-10) cc_final: 0.8364 (m-10)
REVERT: H  128 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8427 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 122
  average time/residue: 0.8387
  time to fit residues: 108.2196
Evaluate side-chains
  119 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain C residue  122 SER
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3378 r_free = 0.3378 target = 0.049701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.033911 restraints weight = 53303.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 1.89
r_work: 0.2621 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12633  Z= 0.197
  Angle     :  0.626  12.490  18299  Z= 0.365
  Chirality :  0.034   0.139   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.516  95.597   4071
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 25.40 %
    Favored  : 73.15 %
  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 (0.31), residues: 730
  helix:  2.81 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.14 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  80 
 TYR   0.010   0.001   TYR B  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (12633)
  covalent geometry    : angle       0.62643 (18299)
  hydrogen bonds       : bond        0.04239 (  753)
  hydrogen bonds       : angle       2.69609 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C   82 ASN cc_start: 0.9328 (t0) cc_final: 0.9126 (t0)
REVERT: C   99 ASP cc_start: 0.8867 (t70) cc_final: 0.8102 (t0)
REVERT: C  101 GLU cc_start: 0.8250 (pm20) cc_final: 0.7774 (pm20)
REVERT: C  121 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8763 (t0)
REVERT: D   91 ASP cc_start: 0.9345 (t0) cc_final: 0.9007 (t0)
REVERT: D   94 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: D  128 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8439 (tp30)
REVERT: G   99 ASP cc_start: 0.9236 (t70) cc_final: 0.8815 (t0)
REVERT: G  121 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8698 (t0)
REVERT: H   58 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8533 (mm-30)
REVERT: H   91 ASP cc_start: 0.9314 (t0) cc_final: 0.8949 (t0)
REVERT: H   94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8557 (tm-30)
REVERT: H  106 TYR cc_start: 0.8772 (m-10) cc_final: 0.8377 (m-80)
REVERT: H  128 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8420 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 121
  average time/residue: 0.7781
  time to fit residues: 99.8735
Evaluate side-chains
  116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 38 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.051099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.035352 restraints weight = 53271.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 1.89
r_work: 0.2676 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12633  Z= 0.157
  Angle     :  0.610  11.479  18299  Z= 0.357
  Chirality :  0.033   0.133   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.050  92.522   4071
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 25.72 %
    Favored  : 73.31 %
  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:  3.42 (0.31), residues: 730
  helix:  2.92 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.02 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 105 
 TYR   0.010   0.001   TYR H  63 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12633)
  covalent geometry    : angle       0.60982 (18299)
  hydrogen bonds       : bond        0.03593 (  753)
  hydrogen bonds       : angle       2.51739 ( 1902)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: C   99 ASP cc_start: 0.8789 (t70) cc_final: 0.7649 (t0)
REVERT: C  101 GLU cc_start: 0.8164 (pm20) cc_final: 0.7788 (pm20)
REVERT: C  121 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8717 (t0)
REVERT: D   91 ASP cc_start: 0.9335 (t0) cc_final: 0.8919 (t0)
REVERT: D   94 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: D  128 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8151 (tm-30)
REVERT: E   81 ASP cc_start: 0.8897 (m-30) cc_final: 0.8489 (t0)
REVERT: E  122 LYS cc_start: 0.9188 (ptpp) cc_final: 0.8975 (ptmm)
REVERT: G   28 MET cc_start: 0.9232 (ptt) cc_final: 0.8903 (ppp)
REVERT: G   99 ASP cc_start: 0.9208 (t70) cc_final: 0.8761 (t0)
REVERT: G  121 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8612 (t0)
REVERT: H   58 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: H   91 ASP cc_start: 0.9290 (t0) cc_final: 0.8903 (t0)
REVERT: H   94 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8521 (tm-30)
REVERT: H  106 TYR cc_start: 0.8720 (m-10) cc_final: 0.8334 (m-10)
REVERT: H  128 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8363 (tm-30)
  outliers start: 6
  outliers final: 4
  residues processed: 129
  average time/residue: 0.8446
  time to fit residues: 115.2304
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue   24 VAL
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
C  82 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.050895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.035124 restraints weight = 53335.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 1.94
r_work: 0.2675 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12633  Z= 0.168
  Angle     :  0.611  12.877  18299  Z= 0.356
  Chirality :  0.033   0.134   2087
  Planarity :  0.004   0.039   1304
  Dihedral  : 31.145  91.026   4071
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 26.37 %
    Favored  : 72.19 %
  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:  3.45 (0.31), residues: 730
  helix:  2.96 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.05 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 105 
 TYR   0.010   0.001   TYR B  88 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.002   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12633)
  covalent geometry    : angle       0.61076 (18299)
  hydrogen bonds       : bond        0.03826 (  753)
  hydrogen bonds       : angle       2.56771 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3550.23 seconds
wall clock time: 61 minutes 10.82 seconds (3670.82 seconds total)