Starting phenix.real_space_refine
on Wed Mar  4 06:22:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wz9_21971/03_2026/6wz9_21971.cif"
  }
  resolution = 2.8
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     296      5.49       5
     S      12      5.16       5
     C    6569      2.51       5
     N    2233      2.21       5
     O    2816      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11926
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 784
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 786
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 784
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 818
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 3050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 3050
          Classifications: {'DNA': 148}
          Link IDs: {'rna3p': 147}
    Chain: "J"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 3018
          Classifications: {'DNA': 148}
          Link IDs: {'rna3p': 147}
  Time building chain proxies: 2.37, per 1000 atoms: 0.20
  Number of scatterers: 11926
  At special positions: 0
  Unit cell: (124.02, 95.4, 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      12     16.00
     P     296     15.00
     O    2816      8.00
     N    2233      7.00
     C    6569      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: 0.95
  Conformation dependent library (CDL) restraints added in 397.7 milliseconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      74.8% alpha, 3.3% beta
      148 base pairs and 269 stacking pairs defined.
    Time for finding SS restraints: 2.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.189A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.738A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 4.265A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.920A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.580A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    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: 3.764A  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 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.331A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.875A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.540A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.297A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.757A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.195A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    411 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      380 hydrogen bonds
      760 hydrogen bond angles
      0 basepair planarities
      148 basepair parallelities
      269 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2091
        1.33 -     1.45: 4337
        1.45 -     1.57: 5701
        1.57 -     1.69: 590
        1.69 -     1.81: 22
  Bond restraints: 12741
  Sorted by residual:
  bond pdb=" C   LEU D  98 "
       pdb=" N   LEU D  99 "
    ideal  model  delta    sigma   weight residual
    1.339  1.263  0.076 5.57e-02 3.22e+02 1.87e+00
  bond pdb=" C3'  DG I -37 "
       pdb=" O3'  DG I -37 "
    ideal  model  delta    sigma   weight residual
    1.422  1.383  0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" C3'  DG I  -6 "
       pdb=" O3'  DG I  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.386  0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CG  LEU H  42 "
       pdb=" CD2 LEU H  42 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.46e+00
  ... (remaining 12736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 18186
        2.23 -     4.47: 283
        4.47 -     6.70: 11
        6.70 -     8.93: 2
        8.93 -    11.17: 2
  Bond angle restraints: 18484
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.17   -8.47 3.00e+00 1.11e-01 7.98e+00
  angle pdb=" N   PRO D 100 "
        pdb=" CA  PRO D 100 "
        pdb=" C   PRO D 100 "
      ideal   model   delta    sigma   weight residual
     110.21  114.73   -4.52 1.64e+00 3.72e-01 7.60e+00
  angle pdb=" N   LYS A  64 "
        pdb=" CA  LYS A  64 "
        pdb=" C   LYS A  64 "
      ideal   model   delta    sigma   weight residual
     111.07  113.91   -2.84 1.07e+00 8.73e-01 7.03e+00
  angle pdb=" CA  LEU G  85 "
        pdb=" CB  LEU G  85 "
        pdb=" CG  LEU G  85 "
      ideal   model   delta    sigma   weight residual
     116.30  125.38   -9.08 3.50e+00 8.16e-02 6.73e+00
  angle pdb=" CA  ILE H  51 "
        pdb=" CB  ILE H  51 "
        pdb=" CG1 ILE H  51 "
      ideal   model   delta    sigma   weight residual
     110.40  114.80   -4.40 1.70e+00 3.46e-01 6.70e+00
  ... (remaining 18479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.12: 5262
       33.12 -    66.24: 1589
       66.24 -    99.36: 31
       99.36 -   132.48: 0
      132.48 -   165.60: 2
  Dihedral angle restraints: 6884
    sinusoidal: 4740
      harmonic: 2144
  Sorted by residual:
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.40  165.60     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.53  139.47     1      3.50e+01 8.16e-04 1.38e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1287
       0.034 -    0.069: 594
       0.069 -    0.103: 178
       0.103 -    0.138: 43
       0.138 -    0.172: 8
  Chirality restraints: 2110
  Sorted by residual:
  chirality pdb=" CA  LYS B  79 "
            pdb=" N   LYS B  79 "
            pdb=" C   LYS B  79 "
            pdb=" CB  LYS B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CA  ILE D  86 "
            pdb=" N   ILE D  86 "
            pdb=" C   ILE D  86 "
            pdb=" CB  ILE D  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.85e-01
  chirality pdb=" CA  ILE H  86 "
            pdb=" N   ILE H  86 "
            pdb=" C   ILE H  86 "
            pdb=" CB  ILE H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 2107 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "   -0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO A  43 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "   -0.029 2.00e-02 2.50e+03   1.22e-02 4.09e+00
        pdb=" N9   DA I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO E  43 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 71
        2.59 -     3.17: 9062
        3.17 -     3.75: 22466
        3.75 -     4.32: 31511
        4.32 -     4.90: 43549
  Nonbonded interactions: 106659
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  29 "
            pdb=" OP1  DT J  30 "
     model   vdw
     2.015 3.040
  nonbonded pdb=" NZ  LYS F  59 "
            pdb=" OE2 GLU F  63 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" NH2 ARG C  20 "
            pdb=" OP1  DG I -42 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OE1 GLU A 105 "
            pdb=" NH2 ARG E 129 "
     model   vdw
     2.298 3.120
  ... (remaining 106654 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' and resid 16 through 116)
  selection = (chain 'G' and resid 16 through 116)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.630
  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:                    0.030
  Process input model:                     13.670
  Find NCS groups from input model:        0.090
  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:7.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
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      :  0.006   0.076  12741  Z= 0.270
  Angle     :  0.743  11.165  18484  Z= 0.457
  Chirality :  0.043   0.172   2110
  Planarity :  0.005   0.052   1312
  Dihedral  : 28.895 165.603   5500
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  4.55 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 722
  helix:  0.56 (0.20), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.33 (0.38), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  83 
 TYR   0.019   0.002   TYR H  37 
 PHE   0.020   0.003   PHE H  67 
 HIS   0.013   0.003   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 (12741)
  covalent geometry    : angle       0.74300 (18484)
  hydrogen bonds       : bond        0.08981 (  791)
  hydrogen bonds       : angle       3.57803 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5531 (mmm) cc_final: 0.5155 (mmm)
REVERT: B   91 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7649 (ttmt)
REVERT: C  108 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7226 (mt)
REVERT: D   31 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6881 (tppt)
REVERT: F   68 ASP cc_start: 0.7377 (m-30) cc_final: 0.6857 (m-30)
REVERT: H   68 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (mt-10)
  outliers start: 14
  outliers final: 3
  residues processed: 161
  average time/residue: 0.8496
  time to fit residues: 144.2262
Evaluate side-chains
  105 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
C  31 HIS
D  44 GLN
D  81 ASN
E  39 HIS
E 108 ASN
E 125 GLN
F  93 GLN
G  31 HIS
G  89 ASN
G 110 ASN
H  44 GLN
H  64 ASN
H  81 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.128772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.113118 restraints weight = 23753.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 0.98
r_work: 0.3829 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12741  Z= 0.184
  Angle     :  0.598   8.457  18484  Z= 0.357
  Chirality :  0.035   0.134   2110
  Planarity :  0.005   0.049   1312
  Dihedral  : 31.320 165.211   4063
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 13.47 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.29), residues: 722
  helix:  1.75 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.90 (0.39), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  96 
 TYR   0.010   0.002   TYR H 118 
 PHE   0.019   0.002   PHE A  67 
 HIS   0.007   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12741)
  covalent geometry    : angle       0.59784 (18484)
  hydrogen bonds       : bond        0.04322 (  791)
  hydrogen bonds       : angle       2.98622 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.6160 (mmm) cc_final: 0.5644 (mmm)
REVERT: A  105 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6223 (tm-30)
REVERT: A  125 GLN cc_start: 0.7644 (mt0) cc_final: 0.7185 (mp10)
REVERT: B   78 ARG cc_start: 0.6997 (mtm180) cc_final: 0.6699 (mtp85)
REVERT: D   31 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6683 (tppt)
REVERT: F   68 ASP cc_start: 0.7797 (m-30) cc_final: 0.7362 (m-30)
REVERT: H   68 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7368 (mp0)
REVERT: H   90 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7236 (mp0)
REVERT: H  113 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6984 (tmtt)
  outliers start: 26
  outliers final: 9
  residues processed: 129
  average time/residue: 0.8045
  time to fit residues: 109.7531
Evaluate side-chains
  109 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  75 HIS
D  81 ASN
E 125 GLN
H  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.126612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.110834 restraints weight = 24235.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 1.01
r_work: 0.3788 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12741  Z= 0.239
  Angle     :  0.639   8.573  18484  Z= 0.377
  Chirality :  0.038   0.145   2110
  Planarity :  0.005   0.046   1312
  Dihedral  : 31.503 163.592   4061
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 16.23 %
    Favored  : 78.90 %
  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:  1.77 (0.30), residues: 722
  helix:  1.78 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.77 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  96 
 TYR   0.012   0.002   TYR H 118 
 PHE   0.019   0.002   PHE A  67 
 HIS   0.020   0.003   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 (12741)
  covalent geometry    : angle       0.63876 (18484)
  hydrogen bonds       : bond        0.05146 (  791)
  hydrogen bonds       : angle       3.13906 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.6074 (mmm) cc_final: 0.5547 (mmm)
REVERT: A  125 GLN cc_start: 0.7793 (mt0) cc_final: 0.7219 (mp10)
REVERT: B   78 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6880 (mtp85)
REVERT: F   68 ASP cc_start: 0.7902 (m-30) cc_final: 0.7436 (m-30)
REVERT: H   68 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7319 (mp0)
REVERT: H   90 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7306 (mp0)
REVERT: H  113 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7034 (tmtt)
  outliers start: 30
  outliers final: 15
  residues processed: 120
  average time/residue: 0.7695
  time to fit residues: 97.9207
Evaluate side-chains
  111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0870
   chunk 28 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  25 ASN
B  27 GLN
E 125 GLN
H  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.129267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.113746 restraints weight = 23970.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 0.98
r_work: 0.3840 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3748 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12741  Z= 0.166
  Angle     :  0.576   7.777  18484  Z= 0.344
  Chirality :  0.034   0.138   2110
  Planarity :  0.004   0.045   1312
  Dihedral  : 31.129 164.329   4061
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 18.51 %
    Favored  : 76.46 %
  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:  2.28 (0.30), residues: 722
  helix:  2.17 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.66 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  32 
 TYR   0.009   0.001   TYR B  88 
 PHE   0.023   0.002   PHE A  67 
 HIS   0.007   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12741)
  covalent geometry    : angle       0.57554 (18484)
  hydrogen bonds       : bond        0.04043 (  791)
  hydrogen bonds       : angle       2.86110 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 107
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5966 (mmm) cc_final: 0.5559 (tmm)
REVERT: A  125 GLN cc_start: 0.7667 (mt0) cc_final: 0.7095 (mp10)
REVERT: B   78 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6664 (mtp85)
REVERT: B   92 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6365 (ptm160)
REVERT: F   68 ASP cc_start: 0.7839 (m-30) cc_final: 0.7386 (m-30)
REVERT: H   90 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7269 (mp0)
REVERT: H  113 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.7042 (tmtt)
  outliers start: 31
  outliers final: 11
  residues processed: 125
  average time/residue: 0.8090
  time to fit residues: 106.9163
Evaluate side-chains
  112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 49 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  27 GLN
E 125 GLN
G  38 ASN
H  44 GLN
H  46 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.128486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.112837 restraints weight = 23999.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 0.99
r_work: 0.3827 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.177
  Angle     :  0.582   7.808  18484  Z= 0.348
  Chirality :  0.034   0.140   2110
  Planarity :  0.004   0.045   1312
  Dihedral  : 31.132 162.991   4057
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 18.51 %
    Favored  : 75.16 %
  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:  2.31 (0.30), residues: 722
  helix:  2.18 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.60 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  96 
 TYR   0.011   0.002   TYR F  51 
 PHE   0.023   0.002   PHE A  67 
 HIS   0.010   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12741)
  covalent geometry    : angle       0.58161 (18484)
  hydrogen bonds       : bond        0.04232 (  791)
  hydrogen bonds       : angle       2.90106 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 107
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6687 (mp10)
REVERT: A   80 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7545 (t)
REVERT: A   90 MET cc_start: 0.5942 (mmm) cc_final: 0.5556 (tmm)
REVERT: A  125 GLN cc_start: 0.7745 (mt0) cc_final: 0.7138 (mp10)
REVERT: A  131 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7795 (mtt180)
REVERT: B   78 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6786 (mtp85)
REVERT: B   95 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7648 (mtp85)
REVERT: C   99 ARG cc_start: 0.7848 (mpt180) cc_final: 0.7572 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7840 (m-30) cc_final: 0.7393 (m-30)
REVERT: F   74 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7556 (tp30)
REVERT: H   90 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7302 (mp0)
REVERT: H  113 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.7066 (tmtt)
  outliers start: 39
  outliers final: 15
  residues processed: 128
  average time/residue: 0.8436
  time to fit residues: 113.9959
Evaluate side-chains
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0770
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.126292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.110548 restraints weight = 24177.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 1.00
r_work: 0.3786 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12741  Z= 0.235
  Angle     :  0.641   8.811  18484  Z= 0.376
  Chirality :  0.037   0.149   2110
  Planarity :  0.005   0.047   1312
  Dihedral  : 31.409 161.851   4057
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 19.48 %
    Favored  : 74.68 %
  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:  1.87 (0.30), residues: 722
  helix:  1.91 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.83 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  35 
 TYR   0.013   0.002   TYR G  50 
 PHE   0.025   0.002   PHE A  67 
 HIS   0.009   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (12741)
  covalent geometry    : angle       0.64076 (18484)
  hydrogen bonds       : bond        0.05190 (  791)
  hydrogen bonds       : angle       3.13098 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 103
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6748 (mp10)
REVERT: A   80 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7548 (t)
REVERT: A  115 LYS cc_start: 0.7472 (mmtp) cc_final: 0.7046 (mtmm)
REVERT: A  120 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6895 (mtt)
REVERT: A  131 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7852 (mtt180)
REVERT: B   78 ARG cc_start: 0.7235 (mtm180) cc_final: 0.6878 (mtp85)
REVERT: B   95 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7582 (mtp85)
REVERT: F   68 ASP cc_start: 0.7819 (m-30) cc_final: 0.7423 (m-30)
REVERT: F   74 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7554 (tp30)
REVERT: H   90 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7360 (mp0)
REVERT: H  113 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7062 (tmtt)
  outliers start: 36
  outliers final: 13
  residues processed: 120
  average time/residue: 0.7954
  time to fit residues: 101.0824
Evaluate side-chains
  117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.2980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
G  38 ASN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.128402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.112792 restraints weight = 24027.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 0.99
r_work: 0.3826 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.173
  Angle     :  0.589   8.080  18484  Z= 0.351
  Chirality :  0.034   0.141   2110
  Planarity :  0.004   0.046   1312
  Dihedral  : 31.196 162.635   4057
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 21.92 %
    Favored  : 72.89 %
  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:  2.09 (0.30), residues: 722
  helix:  2.06 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.81 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  35 
 TYR   0.017   0.001   TYR G  50 
 PHE   0.027   0.002   PHE A  67 
 HIS   0.006   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (12741)
  covalent geometry    : angle       0.58905 (18484)
  hydrogen bonds       : bond        0.04262 (  791)
  hydrogen bonds       : angle       2.97152 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6703 (mp10)
REVERT: A   80 THR cc_start: 0.7850 (OUTLIER) cc_final: 0.7557 (t)
REVERT: A   90 MET cc_start: 0.5927 (mmt) cc_final: 0.5077 (ttm)
REVERT: A  115 LYS cc_start: 0.7388 (mmtp) cc_final: 0.6923 (mtmm)
REVERT: A  120 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6856 (mtt)
REVERT: A  125 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7208 (mp10)
REVERT: A  131 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7806 (mtt180)
REVERT: B   78 ARG cc_start: 0.7148 (mtm180) cc_final: 0.6775 (mtp85)
REVERT: B   95 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7515 (mtp85)
REVERT: C   99 ARG cc_start: 0.7827 (mpt180) cc_final: 0.7554 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7871 (m-30) cc_final: 0.7472 (m-30)
REVERT: F   74 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7612 (tp30)
REVERT: H   90 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7295 (mp0)
  outliers start: 32
  outliers final: 11
  residues processed: 120
  average time/residue: 0.7970
  time to fit residues: 101.3979
Evaluate side-chains
  117 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.128583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.113002 restraints weight = 24000.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 0.98
r_work: 0.3829 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.2909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.177
  Angle     :  0.593   7.968  18484  Z= 0.351
  Chirality :  0.034   0.140   2110
  Planarity :  0.004   0.046   1312
  Dihedral  : 31.121 162.083   4051
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 23.38 %
    Favored  : 72.40 %
  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:  2.15 (0.30), residues: 722
  helix:  2.12 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  35 
 TYR   0.021   0.002   TYR G  50 
 PHE   0.028   0.002   PHE A  67 
 HIS   0.005   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12741)
  covalent geometry    : angle       0.59255 (18484)
  hydrogen bonds       : bond        0.04218 (  791)
  hydrogen bonds       : angle       2.94392 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7560 (t)
REVERT: A   90 MET cc_start: 0.5911 (mmt) cc_final: 0.5137 (ttm)
REVERT: A  115 LYS cc_start: 0.7368 (mmtp) cc_final: 0.6946 (mtmm)
REVERT: A  120 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6804 (mtt)
REVERT: A  125 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7233 (mp10)
REVERT: A  131 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7627 (mtt180)
REVERT: B   78 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6719 (mtp85)
REVERT: B   95 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7633 (mtp85)
REVERT: C   99 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7572 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7870 (m-30) cc_final: 0.7476 (m-30)
REVERT: F   74 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7640 (tp30)
REVERT: H   90 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7303 (mp0)
  outliers start: 26
  outliers final: 12
  residues processed: 117
  average time/residue: 0.8028
  time to fit residues: 99.3659
Evaluate side-chains
  112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 51 optimal weight:    0.1980
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
F  27 GLN
G  38 ASN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.128448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.112888 restraints weight = 24053.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 0.98
r_work: 0.3829 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12741  Z= 0.181
  Angle     :  0.602   7.897  18484  Z= 0.356
  Chirality :  0.034   0.140   2110
  Planarity :  0.004   0.046   1312
  Dihedral  : 31.080 161.596   4051
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.86 %
    Favored  : 72.08 %
  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:  2.10 (0.30), residues: 722
  helix:  2.08 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.85 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  35 
 TYR   0.026   0.002   TYR G  50 
 PHE   0.029   0.002   PHE A  67 
 HIS   0.006   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (12741)
  covalent geometry    : angle       0.60246 (18484)
  hydrogen bonds       : bond        0.04266 (  791)
  hydrogen bonds       : angle       2.98487 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6718 (mp10)
REVERT: A   80 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7508 (t)
REVERT: A   90 MET cc_start: 0.5993 (mmt) cc_final: 0.5155 (ttm)
REVERT: A  115 LYS cc_start: 0.7355 (mmtp) cc_final: 0.6906 (mtmm)
REVERT: A  120 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6827 (mtt)
REVERT: A  125 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7221 (mp10)
REVERT: B   78 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6760 (mtp85)
REVERT: B   95 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7669 (mtp85)
REVERT: C   99 ARG cc_start: 0.7893 (mpt180) cc_final: 0.7624 (mpp-170)
REVERT: D   30 ARG cc_start: 0.7079 (ttm110) cc_final: 0.6795 (ttt180)
REVERT: F   68 ASP cc_start: 0.7865 (m-30) cc_final: 0.7445 (m-30)
REVERT: F   74 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7610 (tp30)
REVERT: H   90 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7338 (mp0)
  outliers start: 25
  outliers final: 13
  residues processed: 112
  average time/residue: 0.7964
  time to fit residues: 94.3693
Evaluate side-chains
  114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.127922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.112370 restraints weight = 24172.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 0.99
r_work: 0.3819 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12741  Z= 0.194
  Angle     :  0.614   8.314  18484  Z= 0.362
  Chirality :  0.035   0.142   2110
  Planarity :  0.005   0.050   1312
  Dihedral  : 31.152 160.987   4051
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.03 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.30), residues: 722
  helix:  1.99 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.92 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  35 
 TYR   0.032   0.002   TYR G  50 
 PHE   0.031   0.002   PHE A  67 
 HIS   0.006   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12741)
  covalent geometry    : angle       0.61402 (18484)
  hydrogen bonds       : bond        0.04470 (  791)
  hydrogen bonds       : angle       3.04084 ( 1969)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6633 (mp10)
REVERT: A   80 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7502 (t)
REVERT: A   90 MET cc_start: 0.5944 (mmt) cc_final: 0.5164 (ttm)
REVERT: A  115 LYS cc_start: 0.7349 (mmtp) cc_final: 0.6934 (mtmm)
REVERT: A  120 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6910 (mtt)
REVERT: A  125 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7245 (mp10)
REVERT: A  133 GLU cc_start: 0.7491 (mp0) cc_final: 0.7192 (mp0)
REVERT: B   78 ARG cc_start: 0.7209 (mtm180) cc_final: 0.6810 (mtp85)
REVERT: B   95 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7870 (mtp85)
REVERT: C   99 ARG cc_start: 0.7831 (mpt180) cc_final: 0.7571 (mpp-170)
REVERT: D   30 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6824 (ttt180)
REVERT: F   68 ASP cc_start: 0.7851 (m-30) cc_final: 0.7414 (m-30)
REVERT: F   74 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7623 (tp30)
REVERT: H   90 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7332 (mp0)
  outliers start: 25
  outliers final: 15
  residues processed: 114
  average time/residue: 0.8305
  time to fit residues: 100.0868
Evaluate side-chains
  120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  113 LYS
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0770
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.128733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.113268 restraints weight = 23996.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 0.98
r_work: 0.3836 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3742 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12741  Z= 0.170
  Angle     :  0.614   8.416  18484  Z= 0.362
  Chirality :  0.034   0.143   2110
  Planarity :  0.005   0.053   1312
  Dihedral  : 31.136 161.248   4051
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 25.16 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.30), residues: 722
  helix:  2.06 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.89 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  35 
 TYR   0.036   0.002   TYR G  50 
 PHE   0.030   0.002   PHE A  67 
 HIS   0.005   0.001   HIS G  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12741)
  covalent geometry    : angle       0.61409 (18484)
  hydrogen bonds       : bond        0.04164 (  791)
  hydrogen bonds       : angle       2.99281 ( 1969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4616.88 seconds
wall clock time: 79 minutes 2.85 seconds (4742.85 seconds total)