Starting phenix.real_space_refine
on Wed Feb  4 16:55:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k45_62046/02_2026/9k45_62046.cif"
  }
  resolution = 2.71
  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=  -0.001 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     289      5.49       5
     S      10      5.16       5
     C    6577      2.51       5
     N    2178      2.21       5
     O    2776      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11830
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 778
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 3, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.45, per 1000 atoms: 0.21
  Number of scatterers: 11830
  At special positions: 0
  Unit cell: (122.1, 80.3, 116.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     289     15.00
     O    2776      8.00
     N    2178      7.00
     C    6577      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: 0.82
  Conformation dependent library (CDL) restraints added in 300.5 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      74.1% alpha, 2.7% beta
      145 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.700A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.643A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.518A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.591A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.662A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 33
    Processing helix  chain 'C' and resid 37 through 49
      removed outlier: 3.813A  pdb=" N   VAL C  41 " --> pdb=" O   PRO C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 85
      removed outlier: 3.762A  pdb=" N   ALA C  60 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU C  85 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 101
    Processing helix  chain 'C' and resid 102 through 109
    Processing helix  chain 'C' and resid 123 through 127
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 147
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.729A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.634A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.524A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.592A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.710A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 33
    Processing helix  chain 'G' and resid 37 through 49
      removed outlier: 3.831A  pdb=" N   VAL G  41 " --> pdb=" O   PRO G  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 56 through 85
      removed outlier: 3.767A  pdb=" N   ALA G  60 " --> pdb=" O   GLY G  56 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU G  85 " --> pdb=" O   ALA G  81 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 101
    Processing helix  chain 'G' and resid 102 through 109
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.134A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.836A  pdb=" N   ARG C  54 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 89 through 90
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113
      removed outlier: 6.415A  pdb=" N   THR C 112 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.163A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 55
      removed outlier: 6.730A  pdb=" N   ARG G  54 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 90

    403 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2013
        1.33 -     1.45: 4213
        1.45 -     1.57: 5816
        1.57 -     1.69: 577
        1.69 -     1.80: 18
  Bond restraints: 12637
  Sorted by residual:
  bond pdb=" O3'  DC J -24 "
       pdb=" P    DC J -23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.652 -0.045 1.50e-02 4.44e+03 8.96e+00
  bond pdb=" O3'  DT J   5 "
       pdb=" P    DG J   6 "
    ideal  model  delta    sigma   weight residual
    1.607  1.651 -0.044 1.50e-02 4.44e+03 8.76e+00
  bond pdb=" O3'  DA I  -9 "
       pdb=" P    DA I  -8 "
    ideal  model  delta    sigma   weight residual
    1.607  1.644 -0.037 1.50e-02 4.44e+03 6.10e+00
  bond pdb=" O3'  DT J   2 "
       pdb=" P    DC J   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.642 -0.035 1.50e-02 4.44e+03 5.46e+00
  bond pdb=" O3'  DC I  -6 "
       pdb=" P    DA I  -5 "
    ideal  model  delta    sigma   weight residual
    1.607  1.635 -0.028 1.50e-02 4.44e+03 3.48e+00
  ... (remaining 12632 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 17451
        1.26 -     2.52: 761
        2.52 -     3.78: 76
        3.78 -     5.04: 17
        5.04 -     6.30: 6
  Bond angle restraints: 18311
  Sorted by residual:
  angle pdb=" O3'  DC I  -6 "
        pdb=" C3'  DC I  -6 "
        pdb=" C2'  DC I  -6 "
      ideal   model   delta    sigma   weight residual
     111.50  105.59    5.91 1.50e+00 4.44e-01 1.55e+01
  angle pdb=" O3'  DA J -28 "
        pdb=" C3'  DA J -28 "
        pdb=" C2'  DA J -28 "
      ideal   model   delta    sigma   weight residual
     111.50  106.72    4.78 1.50e+00 4.44e-01 1.01e+01
  angle pdb=" O3'  DA I  -8 "
        pdb=" C3'  DA I  -8 "
        pdb=" C2'  DA I  -8 "
      ideal   model   delta    sigma   weight residual
     111.50  107.05    4.45 1.50e+00 4.44e-01 8.79e+00
  angle pdb=" O3'  DC J -26 "
        pdb=" C3'  DC J -26 "
        pdb=" C2'  DC J -26 "
      ideal   model   delta    sigma   weight residual
     111.50  107.10    4.40 1.50e+00 4.44e-01 8.61e+00
  angle pdb=" O3'  DG J -27 "
        pdb=" C3'  DG J -27 "
        pdb=" C2'  DG J -27 "
      ideal   model   delta    sigma   weight residual
     111.50  107.11    4.39 1.50e+00 4.44e-01 8.56e+00
  ... (remaining 18306 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.07: 4310
       18.07 -    36.14: 1106
       36.14 -    54.21: 1244
       54.21 -    72.28: 243
       72.28 -    90.35: 22
  Dihedral angle restraints: 6925
    sinusoidal: 4777
      harmonic: 2148
  Sorted by residual:
  dihedral pdb=" CA  THR G  50 "
           pdb=" C   THR G  50 "
           pdb=" N   ALA G  51 "
           pdb=" CA  ALA G  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CB  GLU G  73 "
           pdb=" CG  GLU G  73 "
           pdb=" CD  GLU G  73 "
           pdb=" OE1 GLU G  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.72  -89.72     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.21  -44.21     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 6922 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1673
       0.040 -    0.080: 334
       0.080 -    0.120: 77
       0.120 -    0.160: 9
       0.160 -    0.200: 6
  Chirality restraints: 2099
  Sorted by residual:
  chirality pdb=" C3'  DA I  -8 "
            pdb=" C4'  DA I  -8 "
            pdb=" O3'  DA I  -8 "
            pdb=" C2'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 9.97e-01
  chirality pdb=" C3'  DA J -28 "
            pdb=" C4'  DA J -28 "
            pdb=" O3'  DA J -28 "
            pdb=" C2'  DA J -28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.86    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality pdb=" C3'  DC I  -6 "
            pdb=" C4'  DC I  -6 "
            pdb=" O3'  DC I  -6 "
            pdb=" C2'  DC I  -6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 2096 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  48 "    0.218 9.50e-02 1.11e+02   9.78e-02 6.13e+00
        pdb=" NE  ARG C  48 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  48 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  48 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  48 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  88 "    0.011 2.00e-02 2.50e+03   1.33e-02 3.07e+00
        pdb=" CG  PHE H  88 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  88 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  88 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  88 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  88 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO H 126 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1214
        2.75 -     3.29: 9691
        3.29 -     3.82: 21816
        3.82 -     4.36: 26751
        4.36 -     4.90: 39014
  Nonbonded interactions: 98486
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  29 "
            pdb=" O   PHE G  36 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG  SER C  29 "
            pdb=" O   PHE C  36 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" N   GLU G 103 "
            pdb=" OE1 GLU G 103 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" NH1 ARG B  92 "
            pdb=" OE1 GLU D  99 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" NH1 ARG F  92 "
            pdb=" OE1 GLU H  99 "
     model   vdw
     2.317 3.120
  ... (remaining 98481 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     12.140
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
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   0.045  12637  Z= 0.176
  Angle     :  0.588   6.295  18311  Z= 0.362
  Chirality :  0.036   0.200   2099
  Planarity :  0.005   0.098   1298
  Dihedral  : 28.625  90.350   5537
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 21.31 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.31), residues: 728
  helix:  2.53 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.89 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  48 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.030   0.001   PHE H  88 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (12637)
  covalent geometry    : angle       0.58761 (18311)
  hydrogen bonds       : bond        0.11164 (  751)
  hydrogen bonds       : angle       4.41048 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 0.310 
Fit side-chains
REVERT: D   91 ASP cc_start: 0.8825 (t70) cc_final: 0.8616 (t0)
REVERT: G   46 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9077 (mtmm)
REVERT: H   91 ASP cc_start: 0.8831 (t70) cc_final: 0.8629 (t0)
  outliers start: 6
  outliers final: 3
  residues processed: 150
  average time/residue: 0.8085
  time to fit residues: 128.1338
Evaluate side-chains
  118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain G residue   47 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
D  72 HIS
E  39 HIS
E 108 ASN
H  72 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.067685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.048648 restraints weight = 42149.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.93
r_work: 0.2873 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12637  Z= 0.167
  Angle     :  0.564   6.421  18311  Z= 0.343
  Chirality :  0.033   0.148   2099
  Planarity :  0.004   0.034   1298
  Dihedral  : 30.458  89.689   4077
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 25.32 %
    Favored  : 72.44 %
  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 are not related in a simple way.
  whole:  3.18 (0.31), residues: 728
  helix:  3.01 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.62 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 105 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.020   0.001   PHE D  88 
 HIS   0.002   0.000   HIS C  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12637)
  covalent geometry    : angle       0.56437 (18311)
  hydrogen bonds       : bond        0.04850 (  751)
  hydrogen bonds       : angle       2.73173 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8493 (pm20) cc_final: 0.8229 (pm20)
REVERT: C   76 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8619 (tm-30)
REVERT: D   58 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7821 (mt-10)
REVERT: D   91 ASP cc_start: 0.9282 (t70) cc_final: 0.8764 (t0)
REVERT: D  147 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8103 (p)
REVERT: E   59 GLU cc_start: 0.8474 (pm20) cc_final: 0.8205 (pm20)
REVERT: E   94 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8063 (tp30)
REVERT: G   46 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8787 (mtmm)
REVERT: G   76 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8670 (tm-30)
REVERT: G  110 LYS cc_start: 0.9261 (mmpt) cc_final: 0.9044 (mmpt)
REVERT: H   91 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8876 (t0)
REVERT: H  116 GLU cc_start: 0.8903 (mp0) cc_final: 0.8592 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 129
  average time/residue: 0.7508
  time to fit residues: 102.6339
Evaluate side-chains
  125 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.3764

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.066557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.047826 restraints weight = 42842.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.93
r_work: 0.2844 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12637  Z= 0.171
  Angle     :  0.556   6.554  18311  Z= 0.339
  Chirality :  0.033   0.149   2099
  Planarity :  0.004   0.038   1298
  Dihedral  : 30.372  89.047   4071
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.00 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.40 (0.32), residues: 728
  helix:  3.20 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.64 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 105 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.006   0.001   PHE F  61 
 HIS   0.001   0.000   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12637)
  covalent geometry    : angle       0.55575 (18311)
  hydrogen bonds       : bond        0.05023 (  751)
  hydrogen bonds       : angle       2.69354 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8657 (pm20) cc_final: 0.8372 (pm20)
REVERT: A   94 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8149 (tp30)
REVERT: B   53 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8600 (mp0)
REVERT: C   48 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8413 (tpp-160)
REVERT: C   76 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8624 (tm-30)
REVERT: D   58 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7869 (mt-10)
REVERT: D   91 ASP cc_start: 0.9267 (t70) cc_final: 0.8778 (t0)
REVERT: D  116 GLU cc_start: 0.8973 (mp0) cc_final: 0.8603 (mp0)
REVERT: E   59 GLU cc_start: 0.8639 (pm20) cc_final: 0.8340 (pm20)
REVERT: E   94 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8097 (tp30)
REVERT: F   53 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8595 (mp0)
REVERT: F   84 MET cc_start: 0.8906 (mmm) cc_final: 0.7745 (mmm)
REVERT: G   46 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8773 (mtmm)
REVERT: G   76 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: H   91 ASP cc_start: 0.9239 (t70) cc_final: 0.8700 (t0)
REVERT: H  116 GLU cc_start: 0.8923 (mp0) cc_final: 0.8549 (mp0)
REVERT: H  136 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8576 (mp0)
  outliers start: 18
  outliers final: 8
  residues processed: 128
  average time/residue: 0.7675
  time to fit residues: 103.9179
Evaluate side-chains
  125 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  136 GLU
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
D 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.064871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.045917 restraints weight = 42182.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.98
r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12637  Z= 0.200
  Angle     :  0.572   7.284  18311  Z= 0.348
  Chirality :  0.034   0.153   2099
  Planarity :  0.004   0.040   1298
  Dihedral  : 30.444  88.867   4071
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.00 %
    Favored  : 71.47 %
  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 are not related in a simple way.
  whole:  3.38 (0.32), residues: 728
  helix:  3.25 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.76 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 105 
 TYR   0.009   0.001   TYR H  63 
 PHE   0.024   0.001   PHE H  88 
 HIS   0.004   0.001   HIS G 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (12637)
  covalent geometry    : angle       0.57232 (18311)
  hydrogen bonds       : bond        0.05763 (  751)
  hydrogen bonds       : angle       2.75415 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8553 (pm20)
REVERT: A   94 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8217 (tp30)
REVERT: C   76 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: C  110 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8831 (mmmt)
REVERT: D   58 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7984 (mt-10)
REVERT: D   91 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8820 (t0)
REVERT: E   59 GLU cc_start: 0.8769 (pm20) cc_final: 0.8502 (pm20)
REVERT: E   94 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8172 (tp30)
REVERT: G   76 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8706 (tm-30)
REVERT: G  110 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8961 (mmmt)
REVERT: H   91 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8962 (t0)
REVERT: H  116 GLU cc_start: 0.8970 (mp0) cc_final: 0.8571 (mp0)
  outliers start: 22
  outliers final: 9
  residues processed: 126
  average time/residue: 0.8010
  time to fit residues: 106.5660
Evaluate side-chains
  117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  136 GLU
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.065523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.046679 restraints weight = 42307.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.97
r_work: 0.2816 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12637  Z= 0.159
  Angle     :  0.568   6.887  18311  Z= 0.345
  Chirality :  0.033   0.147   2099
  Planarity :  0.004   0.037   1298
  Dihedral  : 30.413  88.731   4071
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 25.48 %
    Favored  : 71.79 %
  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 are not related in a simple way.
  whole:  3.45 (0.31), residues: 728
  helix:  3.30 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.73 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  23 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.006   0.001   PHE A  78 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12637)
  covalent geometry    : angle       0.56832 (18311)
  hydrogen bonds       : bond        0.05125 (  751)
  hydrogen bonds       : angle       2.66341 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8797 (pm20) cc_final: 0.8547 (pm20)
REVERT: A   94 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8169 (tp30)
REVERT: A  133 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6494 (mt-10)
REVERT: B   31 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8382 (ttpp)
REVERT: C   76 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8636 (tm-30)
REVERT: D   58 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: D   91 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8802 (t0)
REVERT: D  116 GLU cc_start: 0.8912 (mp0) cc_final: 0.8635 (mp0)
REVERT: E   59 GLU cc_start: 0.8767 (pm20) cc_final: 0.8508 (pm20)
REVERT: E   94 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8134 (tp30)
REVERT: G   76 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8653 (tm-30)
REVERT: G  110 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8941 (mmmt)
REVERT: H   91 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8721 (t0)
REVERT: H  116 GLU cc_start: 0.8926 (mp0) cc_final: 0.8571 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 121
  average time/residue: 0.8468
  time to fit residues: 108.2560
Evaluate side-chains
  124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  123 HIS
Chi-restraints excluded: chain D residue   91 ASP
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  135 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
G 121 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.062929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.043601 restraints weight = 42802.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.01
r_work: 0.2728 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  12637  Z= 0.276
  Angle     :  0.625   7.814  18311  Z= 0.374
  Chirality :  0.036   0.151   2099
  Planarity :  0.004   0.040   1298
  Dihedral  : 30.730  89.799   4071
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 24.36 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.07 (0.32), residues: 728
  helix:  3.06 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.01 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  48 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.029   0.002   PHE D  88 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 (12637)
  covalent geometry    : angle       0.62480 (18311)
  hydrogen bonds       : bond        0.06967 (  751)
  hydrogen bonds       : angle       3.02721 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8832 (pm20) cc_final: 0.8504 (pm20)
REVERT: A   94 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8289 (tp30)
REVERT: C   76 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8615 (tm-30)
REVERT: C  104 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8872 (mm-30)
REVERT: D   58 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (mt-10)
REVERT: D   91 ASP cc_start: 0.9308 (t70) cc_final: 0.9046 (t0)
REVERT: D  147 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8219 (p)
REVERT: E   59 GLU cc_start: 0.8823 (pm20) cc_final: 0.8486 (pm20)
REVERT: E   76 GLN cc_start: 0.9064 (tt0) cc_final: 0.8631 (tm-30)
REVERT: E   94 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8242 (tp30)
REVERT: G   48 ARG cc_start: 0.8788 (tpp-160) cc_final: 0.8535 (tpp-160)
REVERT: G   76 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: H   91 ASP cc_start: 0.9296 (t70) cc_final: 0.9014 (t0)
  outliers start: 22
  outliers final: 10
  residues processed: 126
  average time/residue: 0.7656
  time to fit residues: 101.8177
Evaluate side-chains
  119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  145 THR
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0470
   chunk 82 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    0.9884

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.064526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.045225 restraints weight = 42127.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.00
r_work: 0.2781 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12637  Z= 0.164
  Angle     :  0.591   6.975  18311  Z= 0.354
  Chirality :  0.034   0.141   2099
  Planarity :  0.004   0.043   1298
  Dihedral  : 30.566  89.098   4071
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 26.12 %
    Favored  : 70.83 %
  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 are not related in a simple way.
  whole:  3.32 (0.32), residues: 728
  helix:  3.24 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.89 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  23 
 TYR   0.015   0.001   TYR F  51 
 PHE   0.008   0.001   PHE B  61 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12637)
  covalent geometry    : angle       0.59132 (18311)
  hydrogen bonds       : bond        0.05357 (  751)
  hydrogen bonds       : angle       2.71717 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8790 (pm20) cc_final: 0.8507 (pm20)
REVERT: A   94 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8228 (tp30)
REVERT: C   76 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8647 (tm-30)
REVERT: D   58 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8005 (mt-10)
REVERT: D   91 ASP cc_start: 0.9262 (t70) cc_final: 0.8821 (t0)
REVERT: D  147 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8218 (p)
REVERT: E   59 GLU cc_start: 0.8794 (pm20) cc_final: 0.8513 (pm20)
REVERT: E   76 GLN cc_start: 0.8974 (tt0) cc_final: 0.8603 (tm-30)
REVERT: E   94 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8205 (tp30)
REVERT: G   76 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: G  110 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8843 (mmmt)
REVERT: H   91 ASP cc_start: 0.9225 (t70) cc_final: 0.8764 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 130
  average time/residue: 0.8024
  time to fit residues: 110.1300
Evaluate side-chains
  122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  136 GLU
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain G residue  123 HIS
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  136 GLU
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.065140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.046321 restraints weight = 42424.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.98
r_work: 0.2819 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12637  Z= 0.169
  Angle     :  0.583   6.965  18311  Z= 0.352
  Chirality :  0.033   0.150   2099
  Planarity :  0.004   0.039   1298
  Dihedral  : 30.359  88.590   4071
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.04 %
    Favored  : 69.55 %
  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 are not related in a simple way.
  whole:  3.49 (0.31), residues: 728
  helix:  3.35 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.83 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  48 
 TYR   0.013   0.001   TYR C  62 
 PHE   0.006   0.001   PHE B  61 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12637)
  covalent geometry    : angle       0.58337 (18311)
  hydrogen bonds       : bond        0.05001 (  751)
  hydrogen bonds       : angle       2.62861 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8822 (pm20) cc_final: 0.8536 (pm20)
REVERT: A   94 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8139 (tp30)
REVERT: B   31 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8381 (ttpp)
REVERT: C   76 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: D   58 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8006 (mt-10)
REVERT: D   91 ASP cc_start: 0.9250 (t70) cc_final: 0.8792 (t0)
REVERT: D   99 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8795 (mm-30)
REVERT: D  147 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8178 (p)
REVERT: E   59 GLU cc_start: 0.8799 (pm20) cc_final: 0.8510 (pm20)
REVERT: E   76 GLN cc_start: 0.8983 (tt0) cc_final: 0.8628 (tm-30)
REVERT: E   94 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8017 (tp30)
REVERT: G   48 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8511 (tpp-160)
REVERT: G   76 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: H   91 ASP cc_start: 0.9200 (t70) cc_final: 0.8712 (t0)
REVERT: H  116 GLU cc_start: 0.8889 (mp0) cc_final: 0.8545 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 124
  average time/residue: 0.7825
  time to fit residues: 102.6009
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   52 GLU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  136 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 84 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.065250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.046189 restraints weight = 42293.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.00
r_work: 0.2814 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12637  Z= 0.170
  Angle     :  0.582   7.266  18311  Z= 0.351
  Chirality :  0.033   0.146   2099
  Planarity :  0.004   0.038   1298
  Dihedral  : 30.313  88.479   4071
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 27.56 %
    Favored  : 70.35 %
  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 are not related in a simple way.
  whole:  3.59 (0.32), residues: 728
  helix:  3.44 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.83 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  23 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.030   0.001   PHE D  88 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12637)
  covalent geometry    : angle       0.58160 (18311)
  hydrogen bonds       : bond        0.04822 (  751)
  hydrogen bonds       : angle       2.60659 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8832 (pm20) cc_final: 0.8543 (pm20)
REVERT: A   94 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8080 (tp30)
REVERT: B   31 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8370 (ttpp)
REVERT: C   76 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: D   58 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8025 (mt-10)
REVERT: D   91 ASP cc_start: 0.9247 (t70) cc_final: 0.8798 (t0)
REVERT: D  147 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8183 (p)
REVERT: E   59 GLU cc_start: 0.8796 (pm20) cc_final: 0.8505 (pm20)
REVERT: E   76 GLN cc_start: 0.8933 (tt0) cc_final: 0.8582 (tm-30)
REVERT: E   94 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8023 (tp30)
REVERT: G   48 ARG cc_start: 0.8751 (tpp-160) cc_final: 0.8524 (tpp-160)
REVERT: G   76 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: G  110 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8840 (mmmt)
REVERT: H   91 ASP cc_start: 0.9205 (t70) cc_final: 0.8727 (t0)
REVERT: H  116 GLU cc_start: 0.8860 (mp0) cc_final: 0.8503 (mp0)
  outliers start: 13
  outliers final: 11
  residues processed: 121
  average time/residue: 0.9432
  time to fit residues: 120.4756
Evaluate side-chains
  126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   52 GLU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  136 GLU
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.065243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.046260 restraints weight = 42566.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.01
r_work: 0.2812 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12637  Z= 0.172
  Angle     :  0.583   7.159  18311  Z= 0.352
  Chirality :  0.033   0.150   2099
  Planarity :  0.004   0.039   1298
  Dihedral  : 30.266  88.194   4071
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 28.37 %
    Favored  : 69.55 %
  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 are not related in a simple way.
  whole:  3.64 (0.32), residues: 728
  helix:  3.52 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.87 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  23 
 TYR   0.009   0.001   TYR C  62 
 PHE   0.007   0.001   PHE F  61 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12637)
  covalent geometry    : angle       0.58284 (18311)
  hydrogen bonds       : bond        0.04827 (  751)
  hydrogen bonds       : angle       2.61052 ( 1887)

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

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8835 (pm20) cc_final: 0.8545 (pm20)
REVERT: A   76 GLN cc_start: 0.8871 (tt0) cc_final: 0.8472 (tm-30)
REVERT: A   94 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8060 (tp30)
REVERT: B   31 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8375 (ttpp)
REVERT: C   76 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8588 (tm-30)
REVERT: D   58 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8019 (mt-10)
REVERT: D   91 ASP cc_start: 0.9237 (t70) cc_final: 0.8787 (t0)
REVERT: D  147 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8189 (p)
REVERT: E   59 GLU cc_start: 0.8793 (pm20) cc_final: 0.8508 (pm20)
REVERT: E   76 GLN cc_start: 0.8946 (tt0) cc_final: 0.8562 (tm-30)
REVERT: E   94 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7999 (tp30)
REVERT: G   48 ARG cc_start: 0.8733 (tpp-160) cc_final: 0.8484 (tpp-160)
REVERT: G   76 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: G  110 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8850 (mmmt)
REVERT: H   91 ASP cc_start: 0.9186 (t70) cc_final: 0.8701 (t0)
REVERT: H  116 GLU cc_start: 0.8875 (mp0) cc_final: 0.8514 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 124
  average time/residue: 0.8869
  time to fit residues: 116.3273
Evaluate side-chains
  125 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  135 SER
Chi-restraints excluded: chain D residue  146 SER
Chi-restraints excluded: chain D residue  147 SER
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   50 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  146 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 8 optimal weight:    0.4980
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 90 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.063516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.044231 restraints weight = 43108.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.02
r_work: 0.2756 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12637  Z= 0.234
  Angle     :  0.626   8.496  18311  Z= 0.371
  Chirality :  0.035   0.150   2099
  Planarity :  0.004   0.038   1298
  Dihedral  : 30.491  89.097   4071
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 27.72 %
    Favored  : 70.35 %
  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 are not related in a simple way.
  whole:  3.27 (0.32), residues: 728
  helix:  3.24 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.01 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  40 
 TYR   0.010   0.001   TYR C  62 
 PHE   0.031   0.002   PHE H  88 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 (12637)
  covalent geometry    : angle       0.62567 (18311)
  hydrogen bonds       : bond        0.06171 (  751)
  hydrogen bonds       : angle       2.85481 ( 1887)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3470.44 seconds
wall clock time: 59 minutes 43.19 seconds (3583.19 seconds total)