Starting phenix.real_space_refine
on Wed Sep 17 14:15:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gxa_51645/09_2025/9gxa_51645.map"
  }
  resolution = 4.01
  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=   0.000 sd=   0.011
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     224      5.49       5
     S       8      5.16       5
     C    5167      2.51       5
     N    1696      2.21       5
     O    2120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 9215
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 575
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 2, 'TRANS': 68}
    Chain: "B"
      Number of atoms: 516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 516
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 1, 'TRANS': 63}
    Chain: "C"
      Number of atoms: 628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 628
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
    Chain: "E"
      Number of atoms: 628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 628
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "F"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 565
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 1, 'TRANS': 69}
    Chain: "G"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 621
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "H"
      Number of atoms: 541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 541
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 1, 'TRANS': 66}
    Chain: "I"
      Number of atoms: 2292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2292
          Classifications: {'DNA': 112}
          Link IDs: {'rna3p': 111}
    Chain: "J"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 2300
          Classifications: {'DNA': 112}
          Link IDs: {'rna3p': 111}
  Time building chain proxies: 2.34, per 1000 atoms: 0.25
  Number of scatterers: 9215
  At special positions: 0
  Unit cell: (86.92, 113.16, 121.36, 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       8     16.00
     P     224     15.00
     O    2120      8.00
     N    1696      7.00
     C    5167      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: 0.86
  Conformation dependent library (CDL) restraints added in 211.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 2 sheets defined
      78.7% alpha, 0.7% beta
      108 base pairs and 196 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 4.386A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ILE A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   CYS A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 117
    Processing helix  chain 'A' and resid 122 through 133
      removed outlier: 4.191A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 76
    Processing helix  chain 'B' and resid 83 through 90
      removed outlier: 3.520A  pdb=" N   VAL B  86 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  90 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.505A  pdb=" N   PHE C  67 " --> pdb=" O   ARG C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 116
      removed outlier: 3.548A  pdb=" N   LEU C  92 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 134
      removed outlier: 3.649A  pdb=" N   VAL C 126 " --> pdb=" O   PHE C 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 4.272A  pdb=" N   GLU D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG D  67 " --> pdb=" O   GLU D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 94
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.581A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.726A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.622A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.585A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.708A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 63 through 77
      removed outlier: 3.733A  pdb=" N   PHE G  67 " --> pdb=" O   ARG G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 117
    Processing helix  chain 'G' and resid 122 through 134
      removed outlier: 3.729A  pdb=" N   VAL G 126 " --> pdb=" O   PHE G 122 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 29
      removed outlier: 3.807A  pdb=" N   GLY H  28 " --> pdb=" O   ASN H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 30 through 41
      removed outlier: 3.578A  pdb=" N   ILE H  34 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 49 through 76
      removed outlier: 4.219A  pdb=" N   GLU H  53 " --> pdb=" O   LEU H  49 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA H  76 " --> pdb=" O   TYR H  72 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 91
      removed outlier: 3.519A  pdb=" N   VAL H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS H  91 " --> pdb=" O   VAL H  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 86
      removed outlier: 7.361A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'E' and resid 120 through 121

    323 hydrogen bonds defined for protein.
    954 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      258 hydrogen bonds
      516 hydrogen bond angles
      0 basepair planarities
      108 basepair parallelities
      196 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 1.10 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: 1867
        1.33 -     1.45: 3149
        1.45 -     1.57: 4370
        1.57 -     1.69: 446
        1.69 -     1.81: 12
  Bond restraints: 9844
  Sorted by residual:
  bond pdb=" N   THR C 120 "
       pdb=" CA  THR C 120 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.31e-02 5.83e+03 9.75e+00
  bond pdb=" N   VAL C 119 "
       pdb=" CA  VAL C 119 "
    ideal  model  delta    sigma   weight residual
    1.460  1.499 -0.039 1.32e-02 5.74e+03 8.84e+00
  bond pdb=" N   VAL E  82 "
       pdb=" CA  VAL E  82 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.22e-02 6.72e+03 8.77e+00
  bond pdb=" N   THR E  79 "
       pdb=" CA  THR E  79 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.19e-02 7.06e+03 8.73e+00
  bond pdb=" N   ARG C 118 "
       pdb=" CA  ARG C 118 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.31e-02 5.83e+03 8.38e+00
  ... (remaining 9839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 13533
        1.39 -     2.77: 660
        2.77 -     4.16: 55
        4.16 -     5.55: 14
        5.55 -     6.93: 3
  Bond angle restraints: 14265
  Sorted by residual:
  angle pdb=" CA  ASP E  83 "
        pdb=" C   ASP E  83 "
        pdb=" O   ASP E  83 "
      ideal   model   delta    sigma   weight residual
     122.27  117.86    4.41 1.16e+00 7.43e-01 1.44e+01
  angle pdb=" CA  PHE C 122 "
        pdb=" C   PHE C 122 "
        pdb=" N   PRO C 123 "
      ideal   model   delta    sigma   weight residual
     117.67  121.35   -3.68 1.01e+00 9.80e-01 1.32e+01
  angle pdb=" CA  ARG C 118 "
        pdb=" C   ARG C 118 "
        pdb=" O   ARG C 118 "
      ideal   model   delta    sigma   weight residual
     120.96  117.08    3.88 1.09e+00 8.42e-01 1.27e+01
  angle pdb=" N   VAL A 119 "
        pdb=" CA  VAL A 119 "
        pdb=" C   VAL A 119 "
      ideal   model   delta    sigma   weight residual
     112.96  109.63    3.33 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" CA  VAL C 119 "
        pdb=" C   VAL C 119 "
        pdb=" O   VAL C 119 "
      ideal   model   delta    sigma   weight residual
     120.46  117.08    3.38 1.11e+00 8.12e-01 9.25e+00
  ... (remaining 14260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.61: 4220
       35.61 -    71.23: 1110
       71.23 -   106.84: 21
      106.84 -   142.46: 2
      142.46 -   178.07: 2
  Dihedral angle restraints: 5355
    sinusoidal: 3693
      harmonic: 1662
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DA J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.07 -178.07     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I  57 "
           pdb=" C3'  DA I  57 "
           pdb=" O3'  DA I  57 "
           pdb=" P    DT I  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.59  175.41     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J  44 "
           pdb=" C3'  DT J  44 "
           pdb=" O3'  DT J  44 "
           pdb=" P    DT J  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   -0.19 -139.81     1      3.50e+01 8.16e-04 1.38e+01
  ... (remaining 5352 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1317
       0.041 -    0.083: 256
       0.083 -    0.124: 54
       0.124 -    0.165: 6
       0.165 -    0.207: 3
  Chirality restraints: 1636
  Sorted by residual:
  chirality pdb=" CB  VAL C 119 "
            pdb=" CA  VAL C 119 "
            pdb=" CG1 VAL C 119 "
            pdb=" CG2 VAL C 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  VAL E  82 "
            pdb=" CA  VAL E  82 "
            pdb=" CG1 VAL E  82 "
            pdb=" CG2 VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.70e-01
  chirality pdb=" CA  LYS H  31 "
            pdb=" N   LYS H  31 "
            pdb=" C   LYS H  31 "
            pdb=" CB  LYS H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.11e-01
  ... (remaining 1633 not shown)

  Planarity restraints: 1016
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J   5 "   -0.005 2.00e-02 2.50e+03   1.18e-02 3.11e+00
        pdb=" N1   DC J   5 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DC J   5 "   -0.028 2.00e-02 2.50e+03
        pdb=" O2   DC J   5 "    0.019 2.00e-02 2.50e+03
        pdb=" N3   DC J   5 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC J   5 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J   5 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J   5 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "   -0.021 2.00e-02 2.50e+03   9.48e-03 2.47e+00
        pdb=" N9   DA I  17 "    0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  -4 "    0.017 2.00e-02 2.50e+03   9.91e-03 2.21e+00
        pdb=" N1   DC I  -4 "   -0.012 2.00e-02 2.50e+03
        pdb=" C2   DC I  -4 "    0.012 2.00e-02 2.50e+03
        pdb=" O2   DC I  -4 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC I  -4 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DC I  -4 "    0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I  -4 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DC I  -4 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC I  -4 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1013 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 28
        2.52 -     3.12: 6589
        3.12 -     3.71: 17762
        3.71 -     4.31: 22316
        4.31 -     4.90: 31856
  Nonbonded interactions: 78551
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 112 "
            pdb=" OD1 ASP A 125 "
     model   vdw
     1.931 3.460
  nonbonded pdb=" CG2 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.121 3.460
  nonbonded pdb=" OG1 THR F  30 "
            pdb=" OP1  DT I  18 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" NH2 ARG H  36 "
            pdb=" OP2  DG J -44 "
     model   vdw
     2.173 3.120
  nonbonded pdb=" OD2 ASP C 108 "
            pdb=" NH1 ARG C 133 "
     model   vdw
     2.250 3.120
  ... (remaining 78546 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 65 through 134)
  selection = (chain 'C' and resid 65 through 134)
  selection = (chain 'E' and resid 65 through 134)
  selection = (chain 'G' and resid 65 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and resid 26 through 90)
  selection = (chain 'F' and resid 26 through 90)
  selection = (chain 'H' and resid 26 through 90)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.050
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.260
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
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   0.044   9844  Z= 0.228
  Angle     :  0.653   6.932  14265  Z= 0.404
  Chirality :  0.036   0.207   1636
  Planarity :  0.003   0.024   1016
  Dihedral  : 29.322 178.070   4275
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  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:  1.51 (0.35), residues: 558
  helix:  1.74 (0.25), residues: 429
  sheet:  None (None), residues: 0
  loop : -1.55 (0.46), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  67 
 TYR   0.017   0.001   TYR E 110 
 PHE   0.022   0.001   PHE C  78 
 TRP   0.006   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 9844)
  covalent geometry    : angle       0.65253 (14265)
  hydrogen bonds       : bond        0.10209 (  581)
  hydrogen bonds       : angle       4.17625 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.7457 (t80) cc_final: 0.7199 (t80)
REVERT: A   99 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6588 (mp0)
REVERT: A  110 TYR cc_start: 0.8249 (t80) cc_final: 0.7896 (t80)
REVERT: B   44 LYS cc_start: 0.8753 (mmpt) cc_final: 0.8547 (mmmt)
REVERT: B   50 ILE cc_start: 0.8803 (tt) cc_final: 0.8484 (mt)
REVERT: B   59 LYS cc_start: 0.9417 (tmtt) cc_final: 0.8952 (tmtt)
REVERT: C   96 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6725 (tm-30)
REVERT: H   49 LEU cc_start: 0.8649 (tp) cc_final: 0.8151 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1433
  time to fit residues: 31.2787
Evaluate side-chains
  118 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 115 HIS
** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** 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 = 0.3377 r_free = 0.3377 target = 0.044496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.033382 restraints weight = 84109.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.034286 restraints weight = 46309.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.034891 restraints weight = 32067.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.035263 restraints weight = 25370.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.035506 restraints weight = 22044.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9844  Z= 0.232
  Angle     :  0.678  10.310  14265  Z= 0.400
  Chirality :  0.037   0.236   1636
  Planarity :  0.004   0.033   1016
  Dihedral  : 32.616 179.002   3157
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.57 (0.34), residues: 558
  helix:  1.86 (0.25), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.71 (0.44), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 131 
 TYR   0.016   0.002   TYR D  88 
 PHE   0.028   0.002   PHE C  78 
 TRP   0.009   0.001   TRP E  86 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9844)
  covalent geometry    : angle       0.67776 (14265)
  hydrogen bonds       : bond        0.05811 (  581)
  hydrogen bonds       : angle       3.44150 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7134 (mp0)
REVERT: A  107 GLU cc_start: 0.9084 (pt0) cc_final: 0.8688 (pt0)
REVERT: A  110 TYR cc_start: 0.9046 (t80) cc_final: 0.8727 (t80)
REVERT: B   44 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8615 (mmmt)
REVERT: B   59 LYS cc_start: 0.9718 (tmtt) cc_final: 0.9427 (tptt)
REVERT: B   84 MET cc_start: 0.6605 (mmp) cc_final: 0.5898 (mmp)
REVERT: B   85 ASP cc_start: 0.7338 (m-30) cc_final: 0.6847 (m-30)
REVERT: C   73 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8683 (tm-30)
REVERT: C   96 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7483 (tm-30)
REVERT: C  104 HIS cc_start: 0.8477 (m-70) cc_final: 0.8027 (m-70)
REVERT: C  107 GLU cc_start: 0.8951 (pt0) cc_final: 0.8441 (pp20)
REVERT: C  124 LYS cc_start: 0.9345 (pttp) cc_final: 0.8974 (pttp)
REVERT: E   73 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8621 (tm-30)
REVERT: E   87 GLN cc_start: 0.9417 (tt0) cc_final: 0.8717 (mt0)
REVERT: E   89 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8152 (tp-100)
REVERT: E   99 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: F   50 ILE cc_start: 0.9453 (tp) cc_final: 0.9250 (tp)
REVERT: G  101 PHE cc_start: 0.9386 (t80) cc_final: 0.8894 (t80)
REVERT: G  107 GLU cc_start: 0.9228 (pt0) cc_final: 0.8907 (pp20)
REVERT: G  110 TYR cc_start: 0.9352 (t80) cc_final: 0.8857 (t80)
REVERT: G  131 ARG cc_start: 0.9417 (ptm-80) cc_final: 0.9183 (ptm-80)
REVERT: H   53 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9201 (tt0)
REVERT: H   68 ASP cc_start: 0.9116 (t70) cc_final: 0.8803 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1325
  time to fit residues: 26.7745
Evaluate side-chains
  122 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.043221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.032156 restraints weight = 85682.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.033024 restraints weight = 47238.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.033589 restraints weight = 32799.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.033959 restraints weight = 26286.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.034177 restraints weight = 22761.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9844  Z= 0.243
  Angle     :  0.682   8.951  14265  Z= 0.399
  Chirality :  0.037   0.231   1636
  Planarity :  0.004   0.035   1016
  Dihedral  : 32.877 179.513   3157
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  7.56 %
    Favored  : 92.23 %
  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:  1.52 (0.34), residues: 558
  helix:  1.81 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.68 (0.45), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  67 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.023   0.002   PHE C  78 
 TRP   0.008   0.001   TRP E  86 
 HIS   0.006   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 9844)
  covalent geometry    : angle       0.68178 (14265)
  hydrogen bonds       : bond        0.06056 (  581)
  hydrogen bonds       : angle       3.49755 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8517 (t80) cc_final: 0.8280 (t80)
REVERT: A   99 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7189 (mp0)
REVERT: A  110 TYR cc_start: 0.9062 (t80) cc_final: 0.8765 (t80)
REVERT: B   44 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8679 (mmmt)
REVERT: B   59 LYS cc_start: 0.9720 (tmtt) cc_final: 0.9411 (tptt)
REVERT: B   84 MET cc_start: 0.7040 (mmp) cc_final: 0.6398 (mmp)
REVERT: B   85 ASP cc_start: 0.7481 (m-30) cc_final: 0.6844 (m-30)
REVERT: C   73 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8626 (tm-30)
REVERT: C   96 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7553 (tm-30)
REVERT: C  104 HIS cc_start: 0.8451 (m-70) cc_final: 0.8025 (m-70)
REVERT: C  107 GLU cc_start: 0.8989 (pt0) cc_final: 0.8502 (pp20)
REVERT: C  124 LYS cc_start: 0.9329 (pttp) cc_final: 0.8960 (pttp)
REVERT: C  130 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8672 (tpt90)
REVERT: D   44 LYS cc_start: 0.9509 (mmtm) cc_final: 0.9100 (mmtt)
REVERT: D   63 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: D   64 ASN cc_start: 0.9267 (m-40) cc_final: 0.8962 (m-40)
REVERT: D   67 ARG cc_start: 0.8987 (ttp-170) cc_final: 0.8703 (ttp80)
REVERT: E   87 GLN cc_start: 0.9386 (tt0) cc_final: 0.8639 (mt0)
REVERT: E   89 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8083 (tp-100)
REVERT: F   50 ILE cc_start: 0.9410 (tp) cc_final: 0.9106 (tp)
REVERT: F   82 THR cc_start: 0.9244 (m) cc_final: 0.8895 (m)
REVERT: G  101 PHE cc_start: 0.9411 (t80) cc_final: 0.8960 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1261
  time to fit residues: 25.7436
Evaluate side-chains
  118 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.043549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.032601 restraints weight = 85168.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.033516 restraints weight = 46631.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.034099 restraints weight = 32114.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.034476 restraints weight = 25400.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.034646 restraints weight = 21999.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9844  Z= 0.207
  Angle     :  0.663  10.568  14265  Z= 0.389
  Chirality :  0.037   0.239   1636
  Planarity :  0.004   0.032   1016
  Dihedral  : 32.855 179.137   3157
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  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:  1.64 (0.34), residues: 558
  helix:  1.90 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.63 (0.45), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  69 
 TYR   0.024   0.002   TYR E 110 
 PHE   0.020   0.002   PHE C  78 
 TRP   0.008   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 9844)
  covalent geometry    : angle       0.66296 (14265)
  hydrogen bonds       : bond        0.05039 (  581)
  hydrogen bonds       : angle       3.33807 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8564 (t80) cc_final: 0.8301 (t80)
REVERT: A   99 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7323 (mp0)
REVERT: A  107 GLU cc_start: 0.9093 (pt0) cc_final: 0.8665 (pt0)
REVERT: A  110 TYR cc_start: 0.9058 (t80) cc_final: 0.8733 (t80)
REVERT: B   44 LYS cc_start: 0.9091 (mmpt) cc_final: 0.8648 (mmmt)
REVERT: B   59 LYS cc_start: 0.9721 (tmtt) cc_final: 0.9417 (tptt)
REVERT: B   84 MET cc_start: 0.7299 (mmp) cc_final: 0.6840 (mmp)
REVERT: B   85 ASP cc_start: 0.7491 (m-30) cc_final: 0.6707 (m-30)
REVERT: C   73 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8612 (tm-30)
REVERT: C   96 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7502 (tm-30)
REVERT: C  107 GLU cc_start: 0.9018 (pt0) cc_final: 0.8456 (pp20)
REVERT: C  130 ARG cc_start: 0.9129 (ttp80) cc_final: 0.8662 (tpt90)
REVERT: D   44 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9200 (mmtt)
REVERT: D   63 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: D   67 ARG cc_start: 0.8975 (ttp-170) cc_final: 0.8679 (ttp80)
REVERT: D   68 ASP cc_start: 0.8737 (m-30) cc_final: 0.8389 (m-30)
REVERT: E   73 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: E   87 GLN cc_start: 0.9375 (tt0) cc_final: 0.8653 (mt0)
REVERT: E   89 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8019 (tp-100)
REVERT: F   31 LYS cc_start: 0.9475 (mttm) cc_final: 0.9189 (mtpp)
REVERT: F   50 ILE cc_start: 0.9379 (tp) cc_final: 0.9132 (tp)
REVERT: F   82 THR cc_start: 0.9183 (m) cc_final: 0.8966 (m)
REVERT: F   92 ARG cc_start: 0.8507 (tpt-90) cc_final: 0.7900 (tpt-90)
REVERT: G  101 PHE cc_start: 0.9439 (t80) cc_final: 0.8994 (t80)
REVERT: G  107 GLU cc_start: 0.9206 (pt0) cc_final: 0.8766 (pp20)
REVERT: G  110 TYR cc_start: 0.9364 (t80) cc_final: 0.9045 (t80)
REVERT: H   49 LEU cc_start: 0.9170 (tp) cc_final: 0.8588 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1258
  time to fit residues: 24.6898
Evaluate side-chains
  122 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** C  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 115 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.045717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.034827 restraints weight = 82900.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.035772 restraints weight = 45694.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.036410 restraints weight = 31413.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.036759 restraints weight = 24640.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.037055 restraints weight = 21489.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9844  Z= 0.155
  Angle     :  0.647  11.054  14265  Z= 0.375
  Chirality :  0.036   0.169   1636
  Planarity :  0.004   0.032   1016
  Dihedral  : 32.625 179.791   3157
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.61 (0.34), residues: 558
  helix:  1.81 (0.24), residues: 429
  sheet:  None (None), residues: 0
  loop : -1.55 (0.44), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  69 
 TYR   0.023   0.001   TYR E 110 
 PHE   0.019   0.001   PHE D  61 
 TRP   0.010   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9844)
  covalent geometry    : angle       0.64710 (14265)
  hydrogen bonds       : bond        0.03583 (  581)
  hydrogen bonds       : angle       3.06927 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7361 (mp0)
REVERT: A  107 GLU cc_start: 0.9112 (pt0) cc_final: 0.8673 (pt0)
REVERT: A  110 TYR cc_start: 0.9078 (t80) cc_final: 0.8809 (t80)
REVERT: A  131 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8854 (ttp80)
REVERT: B   44 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8670 (mmmt)
REVERT: B   84 MET cc_start: 0.7207 (mmp) cc_final: 0.6873 (mmp)
REVERT: B   85 ASP cc_start: 0.7410 (m-30) cc_final: 0.6671 (m-30)
REVERT: C   73 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: C   96 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: C  107 GLU cc_start: 0.9002 (pt0) cc_final: 0.8529 (pp20)
REVERT: C  130 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8641 (tpt90)
REVERT: D   44 LYS cc_start: 0.9490 (mmtm) cc_final: 0.9218 (mmtt)
REVERT: D   49 LEU cc_start: 0.9499 (mp) cc_final: 0.9275 (mp)
REVERT: D   63 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: D   67 ARG cc_start: 0.8931 (ttp-170) cc_final: 0.8567 (ttp80)
REVERT: E   87 GLN cc_start: 0.9305 (tt0) cc_final: 0.8860 (mt0)
REVERT: E   89 GLN cc_start: 0.8380 (tp-100) cc_final: 0.7877 (tp-100)
REVERT: E  127 GLN cc_start: 0.9027 (mp10) cc_final: 0.8685 (mp10)
REVERT: F   49 LEU cc_start: 0.9528 (mp) cc_final: 0.9313 (tt)
REVERT: F   50 ILE cc_start: 0.9341 (tp) cc_final: 0.9074 (tp)
REVERT: F   82 THR cc_start: 0.9048 (m) cc_final: 0.8635 (p)
REVERT: F   92 ARG cc_start: 0.8499 (tpt-90) cc_final: 0.7995 (tmm160)
REVERT: G  101 PHE cc_start: 0.9371 (t80) cc_final: 0.8901 (t80)
REVERT: G  107 GLU cc_start: 0.9144 (pt0) cc_final: 0.8690 (pp20)
REVERT: G  110 TYR cc_start: 0.9335 (t80) cc_final: 0.9059 (t80)
REVERT: H   31 LYS cc_start: 0.9582 (ptpp) cc_final: 0.9361 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.1285
  time to fit residues: 26.2413
Evaluate side-chains
  123 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.044571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.033690 restraints weight = 84545.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.034616 restraints weight = 46412.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.035216 restraints weight = 31860.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.035592 restraints weight = 25176.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.035879 restraints weight = 21663.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9844  Z= 0.182
  Angle     :  0.644   7.814  14265  Z= 0.377
  Chirality :  0.036   0.156   1636
  Planarity :  0.004   0.030   1016
  Dihedral  : 32.785 179.443   3157
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.78 %
    Favored  : 96.01 %
  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:  1.66 (0.34), residues: 558
  helix:  1.88 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.60 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  69 
 TYR   0.023   0.002   TYR E 110 
 PHE   0.019   0.002   PHE D  61 
 TRP   0.006   0.001   TRP E  86 
 HIS   0.005   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 9844)
  covalent geometry    : angle       0.64364 (14265)
  hydrogen bonds       : bond        0.04463 (  581)
  hydrogen bonds       : angle       3.10277 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9338 (tm-30)
REVERT: A   99 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7385 (mp0)
REVERT: A  107 GLU cc_start: 0.9095 (pt0) cc_final: 0.8655 (pt0)
REVERT: A  110 TYR cc_start: 0.9096 (t80) cc_final: 0.8844 (t80)
REVERT: A  131 ARG cc_start: 0.9147 (ttp80) cc_final: 0.8888 (ttp80)
REVERT: B   44 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8683 (mmmt)
REVERT: B   59 LYS cc_start: 0.9700 (tmtt) cc_final: 0.9425 (tmtt)
REVERT: B   84 MET cc_start: 0.7282 (mmp) cc_final: 0.6901 (mmp)
REVERT: B   85 ASP cc_start: 0.7491 (m-30) cc_final: 0.6627 (m-30)
REVERT: C   73 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: C   96 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7261 (tm-30)
REVERT: C  107 GLU cc_start: 0.9004 (pt0) cc_final: 0.8476 (pp20)
REVERT: C  130 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8637 (tpt90)
REVERT: D   44 LYS cc_start: 0.9503 (mmtm) cc_final: 0.9257 (mmtt)
REVERT: D   63 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: D   67 ARG cc_start: 0.8939 (ttp-170) cc_final: 0.8632 (ttp80)
REVERT: E   87 GLN cc_start: 0.9359 (tt0) cc_final: 0.8991 (mt0)
REVERT: E   89 GLN cc_start: 0.8443 (tp-100) cc_final: 0.7954 (tp-100)
REVERT: E   96 GLU cc_start: 0.8942 (tp30) cc_final: 0.8678 (tp30)
REVERT: F   50 ILE cc_start: 0.9385 (tp) cc_final: 0.9103 (tp)
REVERT: F   82 THR cc_start: 0.9078 (m) cc_final: 0.8741 (p)
REVERT: G  101 PHE cc_start: 0.9327 (t80) cc_final: 0.8967 (t80)
REVERT: G  107 GLU cc_start: 0.9164 (pt0) cc_final: 0.8803 (pp20)
REVERT: H   31 LYS cc_start: 0.9581 (ptpp) cc_final: 0.9331 (pttm)
REVERT: H   49 LEU cc_start: 0.9187 (tp) cc_final: 0.8646 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 149
  average time/residue: 0.1335
  time to fit residues: 25.4476
Evaluate side-chains
  121 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    0.2980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.045725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.034878 restraints weight = 84285.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.035830 restraints weight = 46789.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.036442 restraints weight = 32184.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.036835 restraints weight = 25380.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.037100 restraints weight = 21853.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9844  Z= 0.158
  Angle     :  0.655   9.069  14265  Z= 0.378
  Chirality :  0.036   0.174   1636
  Planarity :  0.003   0.032   1016
  Dihedral  : 32.680 178.941   3157
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  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:  1.64 (0.34), residues: 558
  helix:  1.89 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop : -1.64 (0.42), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  69 
 TYR   0.026   0.002   TYR E 110 
 PHE   0.019   0.001   PHE D  61 
 TRP   0.007   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9844)
  covalent geometry    : angle       0.65479 (14265)
  hydrogen bonds       : bond        0.03690 (  581)
  hydrogen bonds       : angle       3.04287 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9298 (tm-30)
REVERT: A   99 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7397 (mp0)
REVERT: A  107 GLU cc_start: 0.9109 (pt0) cc_final: 0.8645 (pt0)
REVERT: A  110 TYR cc_start: 0.9093 (t80) cc_final: 0.8874 (t80)
REVERT: A  131 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8890 (ttp80)
REVERT: B   44 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8715 (mmmt)
REVERT: B   84 MET cc_start: 0.7161 (mmp) cc_final: 0.6826 (mmp)
REVERT: B   85 ASP cc_start: 0.7340 (m-30) cc_final: 0.6603 (m-30)
REVERT: C   73 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8591 (tm-30)
REVERT: C   96 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7254 (tm-30)
REVERT: C  107 GLU cc_start: 0.8984 (pt0) cc_final: 0.8546 (pp20)
REVERT: C  130 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8649 (tpt90)
REVERT: D   44 LYS cc_start: 0.9459 (mmtm) cc_final: 0.9233 (mmtt)
REVERT: D   63 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: D   67 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8552 (ttp80)
REVERT: D   74 GLU cc_start: 0.9190 (tp30) cc_final: 0.8986 (tm-30)
REVERT: E   87 GLN cc_start: 0.9346 (tt0) cc_final: 0.9000 (mt0)
REVERT: E   89 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7882 (tp-100)
REVERT: F   49 LEU cc_start: 0.9291 (tt) cc_final: 0.8424 (tp)
REVERT: F   50 ILE cc_start: 0.9341 (tp) cc_final: 0.8931 (tp)
REVERT: F   82 THR cc_start: 0.9224 (m) cc_final: 0.8782 (p)
REVERT: G  101 PHE cc_start: 0.9328 (t80) cc_final: 0.8974 (t80)
REVERT: G  107 GLU cc_start: 0.9171 (pt0) cc_final: 0.8850 (pp20)
REVERT: G  108 ASP cc_start: 0.8807 (m-30) cc_final: 0.7574 (m-30)
REVERT: H   39 ARG cc_start: 0.8998 (tpt90) cc_final: 0.8534 (tpt90)
REVERT: H   44 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8653 (mmmm)
REVERT: H   49 LEU cc_start: 0.9087 (tp) cc_final: 0.8572 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1388
  time to fit residues: 27.1371
Evaluate side-chains
  121 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.3375 r_free = 0.3375 target = 0.044100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.033287 restraints weight = 84351.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.034213 restraints weight = 46836.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.034809 restraints weight = 32269.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.035192 restraints weight = 25431.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.035471 restraints weight = 21955.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9844  Z= 0.196
  Angle     :  0.664   7.517  14265  Z= 0.386
  Chirality :  0.037   0.156   1636
  Planarity :  0.004   0.041   1016
  Dihedral  : 32.867 179.923   3157
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.64 (0.34), residues: 558
  helix:  1.90 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop : -1.71 (0.43), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G 131 
 TYR   0.025   0.002   TYR E 110 
 PHE   0.021   0.002   PHE D  61 
 TRP   0.005   0.001   TRP E  86 
 HIS   0.005   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9844)
  covalent geometry    : angle       0.66423 (14265)
  hydrogen bonds       : bond        0.04682 (  581)
  hydrogen bonds       : angle       3.21105 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7675 (mt-10)
REVERT: A  107 GLU cc_start: 0.9123 (pt0) cc_final: 0.8675 (pt0)
REVERT: A  110 TYR cc_start: 0.9091 (t80) cc_final: 0.8859 (t80)
REVERT: B   44 LYS cc_start: 0.9101 (mmpt) cc_final: 0.8714 (mmmt)
REVERT: B   59 LYS cc_start: 0.9706 (tmtt) cc_final: 0.9315 (tmtt)
REVERT: B   84 MET cc_start: 0.7354 (mmp) cc_final: 0.6942 (mmp)
REVERT: B   85 ASP cc_start: 0.7507 (m-30) cc_final: 0.6637 (m-30)
REVERT: C   73 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: C   96 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7258 (tm-30)
REVERT: C  107 GLU cc_start: 0.9004 (pt0) cc_final: 0.8493 (pp20)
REVERT: C  130 ARG cc_start: 0.9182 (ttp80) cc_final: 0.8668 (tpt90)
REVERT: D   63 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: D   67 ARG cc_start: 0.8924 (ttp-170) cc_final: 0.8609 (ttp80)
REVERT: E   87 GLN cc_start: 0.9361 (tt0) cc_final: 0.8972 (mt0)
REVERT: E   89 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8028 (tp-100)
REVERT: E   96 GLU cc_start: 0.8908 (tp30) cc_final: 0.8700 (tt0)
REVERT: F   49 LEU cc_start: 0.9136 (tt) cc_final: 0.8622 (tp)
REVERT: F   50 ILE cc_start: 0.9390 (tp) cc_final: 0.8978 (tp)
REVERT: F   82 THR cc_start: 0.9248 (m) cc_final: 0.8808 (p)
REVERT: G  101 PHE cc_start: 0.9338 (t80) cc_final: 0.9026 (t80)
REVERT: G  107 GLU cc_start: 0.9208 (pt0) cc_final: 0.8907 (pp20)
REVERT: G  110 TYR cc_start: 0.9284 (t80) cc_final: 0.8987 (t80)
REVERT: H   39 ARG cc_start: 0.9032 (tpt90) cc_final: 0.8571 (tpt90)
REVERT: H   44 LYS cc_start: 0.9069 (mmmm) cc_final: 0.8640 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1279
  time to fit residues: 24.1378
Evaluate side-chains
  119 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 63 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.042546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.031686 restraints weight = 85075.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.032583 restraints weight = 47216.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.033190 restraints weight = 32625.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.033518 restraints weight = 25743.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.033762 restraints weight = 22545.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9844  Z= 0.244
  Angle     :  0.702   7.678  14265  Z= 0.407
  Chirality :  0.038   0.160   1636
  Planarity :  0.004   0.029   1016
  Dihedral  : 33.170 177.804   3157
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  1.42 (0.34), residues: 558
  helix:  1.72 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.76 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A  69 
 TYR   0.024   0.002   TYR E 110 
 PHE   0.022   0.002   PHE D  61 
 TRP   0.004   0.001   TRP E  86 
 HIS   0.011   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 9844)
  covalent geometry    : angle       0.70232 (14265)
  hydrogen bonds       : bond        0.05984 (  581)
  hydrogen bonds       : angle       3.46864 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.8931 (mmp80) cc_final: 0.8730 (mmp80)
REVERT: A   99 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7566 (mt-10)
REVERT: A  107 GLU cc_start: 0.9134 (pt0) cc_final: 0.8697 (pt0)
REVERT: A  110 TYR cc_start: 0.9069 (t80) cc_final: 0.8790 (t80)
REVERT: B   44 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8720 (mmmt)
REVERT: B   84 MET cc_start: 0.7600 (mmp) cc_final: 0.7265 (mmp)
REVERT: B   85 ASP cc_start: 0.7407 (m-30) cc_final: 0.6665 (m-30)
REVERT: C   73 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8622 (tm-30)
REVERT: C   96 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: C  107 GLU cc_start: 0.9012 (pt0) cc_final: 0.8547 (pp20)
REVERT: C  130 ARG cc_start: 0.9183 (ttp80) cc_final: 0.8692 (tpt90)
REVERT: D   63 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: D   67 ARG cc_start: 0.8936 (ttp-170) cc_final: 0.8590 (ttp80)
REVERT: E   87 GLN cc_start: 0.9309 (tt0) cc_final: 0.8853 (mt0)
REVERT: E   89 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8054 (tp-100)
REVERT: E   96 GLU cc_start: 0.8936 (tp30) cc_final: 0.8670 (tp30)
REVERT: F   49 LEU cc_start: 0.9162 (tt) cc_final: 0.8898 (tt)
REVERT: F   50 ILE cc_start: 0.9386 (tp) cc_final: 0.8914 (tp)
REVERT: G  101 PHE cc_start: 0.9284 (t80) cc_final: 0.9075 (t80)
REVERT: G  107 GLU cc_start: 0.9212 (pt0) cc_final: 0.8891 (pp20)
REVERT: H   39 ARG cc_start: 0.9004 (tpt90) cc_final: 0.8593 (tpt90)
REVERT: H   44 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8750 (mmmt)
REVERT: H   49 LEU cc_start: 0.9155 (tp) cc_final: 0.8612 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1299
  time to fit residues: 23.3787
Evaluate side-chains
  112 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 38 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3375 r_free = 0.3375 target = 0.044071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.033363 restraints weight = 84234.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.034308 restraints weight = 46856.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.034922 restraints weight = 32097.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.035308 restraints weight = 25133.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.035583 restraints weight = 21592.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9844  Z= 0.172
  Angle     :  0.680  10.418  14265  Z= 0.390
  Chirality :  0.037   0.152   1636
  Planarity :  0.004   0.063   1016
  Dihedral  : 32.975 179.244   3157
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  1.46 (0.34), residues: 558
  helix:  1.73 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.66 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  69 
 TYR   0.022   0.002   TYR E 110 
 PHE   0.020   0.002   PHE D  61 
 TRP   0.008   0.001   TRP E  86 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9844)
  covalent geometry    : angle       0.68025 (14265)
  hydrogen bonds       : bond        0.04189 (  581)
  hydrogen bonds       : angle       3.20373 ( 1470)

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

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

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1116 Ramachandran restraints generated.
    558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7325 (mp0)
REVERT: A  107 GLU cc_start: 0.9138 (pt0) cc_final: 0.8696 (pt0)
REVERT: A  110 TYR cc_start: 0.9049 (t80) cc_final: 0.8806 (t80)
REVERT: B   44 LYS cc_start: 0.9108 (mmpt) cc_final: 0.8738 (mmmt)
REVERT: B   59 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9166 (tmtt)
REVERT: B   84 MET cc_start: 0.7622 (mmp) cc_final: 0.7193 (mmp)
REVERT: B   85 ASP cc_start: 0.7472 (m-30) cc_final: 0.6549 (m-30)
REVERT: C   73 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8625 (tm-30)
REVERT: C   96 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7231 (tm-30)
REVERT: C  107 GLU cc_start: 0.8993 (pt0) cc_final: 0.8479 (pp20)
REVERT: C  130 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8647 (tpt90)
REVERT: D   63 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: D   67 ARG cc_start: 0.8935 (ttp-170) cc_final: 0.8607 (ttp80)
REVERT: E   87 GLN cc_start: 0.9390 (tt0) cc_final: 0.9049 (mt0)
REVERT: E   89 GLN cc_start: 0.8396 (tp-100) cc_final: 0.7944 (tp-100)
REVERT: F   49 LEU cc_start: 0.9269 (tt) cc_final: 0.8734 (tt)
REVERT: F   50 ILE cc_start: 0.9331 (tp) cc_final: 0.8859 (tp)
REVERT: F   82 THR cc_start: 0.9211 (m) cc_final: 0.8774 (p)
REVERT: G  108 ASP cc_start: 0.8757 (m-30) cc_final: 0.8533 (m-30)
REVERT: G  110 TYR cc_start: 0.9223 (t80) cc_final: 0.8943 (t80)
REVERT: H   39 ARG cc_start: 0.9015 (tpt90) cc_final: 0.8596 (tpt90)
REVERT: H   44 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8703 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1286
  time to fit residues: 24.1044
Evaluate side-chains
  116 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 64 optimal weight:    8.9990
   chunk 71 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3314 r_free = 0.3314 target = 0.041734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.030924 restraints weight = 86315.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.031746 restraints weight = 48905.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.032307 restraints weight = 34267.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.032674 restraints weight = 27131.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.032891 restraints weight = 23494.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9844  Z= 0.278
  Angle     :  0.728   8.156  14265  Z= 0.420
  Chirality :  0.039   0.189   1636
  Planarity :  0.004   0.038   1016
  Dihedral  : 33.382 176.999   3157
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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:  1.14 (0.34), residues: 558
  helix:  1.53 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 131 
 TYR   0.024   0.003   TYR E 110 
 PHE   0.023   0.002   PHE H  61 
 TRP   0.004   0.001   TRP E  86 
 HIS   0.005   0.001   HIS E 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00607 ( 9844)
  covalent geometry    : angle       0.72753 (14265)
  hydrogen bonds       : bond        0.06767 (  581)
  hydrogen bonds       : angle       3.60258 ( 1470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1654.76 seconds
wall clock time: 29 minutes 15.43 seconds (1755.43 seconds total)