Starting phenix.real_space_refine
on Tue Feb  3 20:40:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zk3_60172/02_2026/8zk3_60172.cif"
  }
  resolution = 3.8
  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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4260      2.51       5
     N    1153      2.21       5
     O    1280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  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: 6729
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1685
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201}
    Chain: "B"
      Number of atoms: 1676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1676
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200}
    Chain: "D"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1586
          Classifications: {'peptide': 203}
          Link IDs: {'CIS': 10, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 181}
    Chain: "G"
      Number of atoms: 1782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1782
          Classifications: {'peptide': 224}
          Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 210}
  Residues with excluded nonbonded symmetry interactions: 92
    residue:
      pdb=" N   GLN A  29 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NE2 GLN A  29 " occ=0.97
    residue:
      pdb=" N   THR A  48 " occ=0.83
      ... (5 atoms not shown)
      pdb=" CG2 THR A  48 " occ=0.83
    residue:
      pdb=" N   CYS A  51 " occ=0.91
      ... (4 atoms not shown)
      pdb=" SG  CYS A  51 " occ=0.91
    residue:
      pdb=" N   LEU A 163 " occ=0.96
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 163 " occ=0.96
    residue:
      pdb=" N   LYS A 190 " occ=0.69
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 190 " occ=0.69
    residue:
      pdb=" N   LYS A 229 " occ=0.80
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 229 " occ=0.80
    residue:
      pdb=" N   GLU A 231 " occ=0.45
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 231 " occ=0.45
    residue:
      pdb=" N   ALA B  59 " occ=0.99
      ... (3 atoms not shown)
      pdb=" CB  ALA B  59 " occ=0.20
    residue:
      pdb=" N   SER B 100 " occ=0.28
      ... (4 atoms not shown)
      pdb=" OG  SER B 100 " occ=0.64
    residue:
      pdb=" N   GLY B 130 " occ=0.97
      ... (2 atoms not shown)
      pdb=" O   GLY B 130 " occ=0.00
    residue:
      pdb=" N   LYS B 148 " occ=0.96
      ... (7 atoms not shown)
      pdb=" NZ  LYS B 148 " occ=0.96
    residue:
      pdb=" N   GLU B 231 " occ=0.97
      ... (7 atoms not shown)
      pdb=" OE2 GLU B 231 " occ=0.97
    ... (remaining 80 not shown)
  Time building chain proxies: 1.65, per 1000 atoms: 0.25
  Number of scatterers: 6729
  At special positions: 0
  Unit cell: (118.483, 128.266, 101.091, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1280      8.00
     N    1153      7.00
     C    4260      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 125 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 219 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B 125 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 165 " - pdb=" SG  CYS B 219 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 154 " - pdb=" SG  CYS G 210 " distance=2.04

  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: 0.60
  Conformation dependent library (CDL) restraints added in 252.1 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1578

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 20 sheets defined
      3.0% alpha, 37.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 89 through 93
    Processing helix  chain 'B' and resid 102 through 106
    Processing helix  chain 'D' and resid 29 through 33
      removed outlier: 3.669A  pdb=" N   ASN D  32 " --> pdb=" O   ALA D  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 88 through 92
    Processing helix  chain 'G' and resid 201 through 206
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
      removed outlier: 3.928A  pdb=" N   ALA A 109 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41
      removed outlier: 6.326A  pdb=" N   ILE A  39 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 156
      removed outlier: 6.274A  pdb=" N   ARG A 162 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 186
      removed outlier: 3.529A  pdb=" N   ALA A 186 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   TRP A 178 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 33
      removed outlier: 4.091A  pdb=" N   ALA B 109 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78
    Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 156
      removed outlier: 3.819A  pdb=" N   ILE B 166 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ARG B 162 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLU B 164 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   VAL B 207 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ILE B 166 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   THR B 205 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   ARG B 168 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B 203 " --> pdb=" O   ARG B 168 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   LYS B 190 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 179
    Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 24
    Processing sheet with id=AB1, first strand: chain 'D' and resid 47 through 50
      removed outlier: 5.154A  pdb=" N   PHE D  48 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ARG D  39 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 50
      removed outlier: 5.154A  pdb=" N   PHE D  48 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ARG D  39 " --> pdb=" O   PHE D  48 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE D 108 " --> pdb=" O   SER D  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 133
      removed outlier: 3.658A  pdb=" N   ALA D 139 " --> pdb=" O   MET D 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 151 through 153
      removed outlier: 3.792A  pdb=" N   VAL D 193 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL D 200 " --> pdb=" O   VAL D 193 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 168
      removed outlier: 4.727A  pdb=" N   GLU D 162 " --> pdb=" O   LYS D 182 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LYS D 182 " --> pdb=" O   GLU D 162 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   ASP D 164 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   LEU D 180 " --> pdb=" O   ASP D 164 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'G' and resid 3 through 5
    Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 13
      removed outlier: 3.591A  pdb=" N   ALA G  93 " --> pdb=" O   LEU G 119 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL G  50 " --> pdb=" O   TRP G  37 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 13
      removed outlier: 3.591A  pdb=" N   ALA G  93 " --> pdb=" O   LEU G 119 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 134 through 135
    Processing sheet with id=AC1, first strand: chain 'G' and resid 134 through 135
      removed outlier: 3.975A  pdb=" N   MET G 185 " --> pdb=" O   MET G 192 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'G' and resid 165 through 169
      removed outlier: 3.594A  pdb=" N   LYS G 165 " --> pdb=" O   ARG G 213 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   HIS G 167 " --> pdb=" O   ILE G 211 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE G 211 " --> pdb=" O   HIS G 167 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    522 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2198
        1.35 -     1.47: 1610
        1.47 -     1.59: 3009
        1.59 -     1.72: 0
        1.72 -     1.84: 56
  Bond restraints: 6873
  Sorted by residual:
  bond pdb=" CA  ARG G  59 "
       pdb=" CB  ARG G  59 "
    ideal  model  delta    sigma   weight residual
    1.526  1.550 -0.024 1.53e-02 4.27e+03 2.43e+00
  bond pdb=" C   GLY G 114 "
       pdb=" N   PRO G 115 "
    ideal  model  delta    sigma   weight residual
    1.334  1.324  0.009 8.40e-03 1.42e+04 1.27e+00
  bond pdb=" N   GLY D 135 "
       pdb=" CA  GLY D 135 "
    ideal  model  delta    sigma   weight residual
    1.453  1.443  0.009 8.60e-03 1.35e+04 1.16e+00
  bond pdb=" N   GLY B 146 "
       pdb=" CA  GLY B 146 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.008 7.70e-03 1.69e+04 1.16e+00
  bond pdb=" C   ILE G  74 "
       pdb=" N   PRO G  75 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.025 2.34e-02 1.83e+03 1.12e+00
  ... (remaining 6868 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 9137
        2.28 -     4.56: 145
        4.56 -     6.84: 9
        6.84 -     9.12: 9
        9.12 -    11.41: 2
  Bond angle restraints: 9302
  Sorted by residual:
  angle pdb=" C   MET D  25 "
        pdb=" N   LYS D  26 "
        pdb=" CA  LYS D  26 "
      ideal   model   delta    sigma   weight residual
     121.70  133.11  -11.41 1.80e+00 3.09e-01 4.02e+01
  angle pdb=" C   ARG D  85 "
        pdb=" N   ASP D  86 "
        pdb=" CA  ASP D  86 "
      ideal   model   delta    sigma   weight residual
     121.70  131.68   -9.98 1.80e+00 3.09e-01 3.08e+01
  angle pdb=" C   ASN G 217 "
        pdb=" N   LYS G 218 "
        pdb=" CA  LYS G 218 "
      ideal   model   delta    sigma   weight residual
     121.70  130.30   -8.60 1.80e+00 3.09e-01 2.28e+01
  angle pdb=" C   GLY D 101 "
        pdb=" N   GLU D 102 "
        pdb=" CA  GLU D 102 "
      ideal   model   delta    sigma   weight residual
     121.70  129.46   -7.76 1.80e+00 3.09e-01 1.86e+01
  angle pdb=" C   GLU D  84 "
        pdb=" N   ARG D  85 "
        pdb=" CA  ARG D  85 "
      ideal   model   delta    sigma   weight residual
     121.70  129.44   -7.74 1.80e+00 3.09e-01 1.85e+01
  ... (remaining 9297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3633
       17.92 -    35.84: 431
       35.84 -    53.76: 87
       53.76 -    71.69: 21
       71.69 -    89.61: 7
  Dihedral angle restraints: 4179
    sinusoidal: 1719
      harmonic: 2460
  Sorted by residual:
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  92 "
           pdb=" CB  CYS D  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.05  -43.05     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" CA  VAL D 142 "
           pdb=" C   VAL D 142 "
           pdb=" N   LYS D 143 "
           pdb=" CA  LYS D 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  ARG A 124 "
           pdb=" C   ARG A 124 "
           pdb=" N   CYS A 125 "
           pdb=" CA  CYS A 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.38   19.62     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 610
       0.032 -    0.063: 268
       0.063 -    0.095: 87
       0.095 -    0.126: 59
       0.126 -    0.158: 11
  Chirality restraints: 1035
  Sorted by residual:
  chirality pdb=" CA  ILE G 110 "
            pdb=" N   ILE G 110 "
            pdb=" C   ILE G 110 "
            pdb=" CB  ILE G 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" CA  VAL D 131 "
            pdb=" N   VAL D 131 "
            pdb=" C   VAL D 131 "
            pdb=" CB  VAL D 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE B 221 "
            pdb=" N   ILE B 221 "
            pdb=" C   ILE B 221 "
            pdb=" CB  ILE B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 1032 not shown)

  Planarity restraints: 1196
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  57 "    0.044 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO D  58 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO D  58 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  58 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS G 133 "   -0.043 5.00e-02 4.00e+02   6.56e-02 6.88e+00
        pdb=" N   PRO G 134 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO G 134 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO G 134 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  72 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.84e+00
        pdb=" N   PRO A  73 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1193 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 134
        2.62 -     3.19: 5975
        3.19 -     3.76: 9397
        3.76 -     4.33: 12928
        4.33 -     4.90: 22211
  Nonbonded interactions: 50645
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  58 "
            pdb=" OG  SER B 104 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" OH  TYR B  92 "
            pdb=" OH  TYR B 123 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OG  SER G  34 "
            pdb=" OG  SER G  53 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" OH  TYR G  38 "
            pdb=" NZ  LYS G 111 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" O   GLU G 143 "
            pdb=" OG1 THR G 144 "
     model   vdw
     2.160 3.040
  ... (remaining 50640 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 30 through 242)
  selection = chain 'B'
}

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=0.75
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.930
  Find NCS groups from input model:        0.070
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
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   0.031   6880  Z= 0.173
  Angle     :  0.749  11.406   9316  Z= 0.427
  Chirality :  0.046   0.158   1035
  Planarity :  0.005   0.068   1196
  Dihedral  : 16.351  89.608   2580
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 20.27 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -4.04 (0.25), residues: 846
  helix:  None (None), residues: 0
  sheet: -2.47 (0.24), residues: 350
  loop : -2.91 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  85 
 TYR   0.015   0.001   TYR A 126 
 PHE   0.008   0.001   PHE D  60 
 TRP   0.006   0.001   TRP G  37 
 HIS   0.003   0.001   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6873)
  covalent geometry    : angle       0.74894 ( 9302)
  SS BOND              : bond        0.00604 (    7)
  SS BOND              : angle       1.05781 (   14)
  hydrogen bonds       : bond        0.13635 (  207)
  hydrogen bonds       : angle       7.24546 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   62 MET cc_start: 0.7387 (mtt) cc_final: 0.7157 (mtt)
REVERT: A  228 GLN cc_start: 0.8936 (mt0) cc_final: 0.8561 (mt0)
REVERT: B   61 ASP cc_start: 0.8928 (p0) cc_final: 0.8321 (p0)
REVERT: B  123 TYR cc_start: 0.9159 (m-80) cc_final: 0.8927 (m-80)
REVERT: B  222 ASN cc_start: 0.8755 (p0) cc_final: 0.8472 (p0)
REVERT: D   15 ILE cc_start: 0.6786 (mp) cc_final: 0.6540 (mp)
REVERT: D   60 PHE cc_start: 0.8612 (m-80) cc_final: 0.7479 (m-80)
REVERT: D   76 VAL cc_start: 0.7087 (t) cc_final: 0.6861 (p)
REVERT: G   17 LYS cc_start: 0.9472 (mmtm) cc_final: 0.9036 (tttm)
  outliers start: 7
  outliers final: 3
  residues processed: 133
  average time/residue: 0.0970
  time to fit residues: 16.6917
Evaluate side-chains
  118 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain G residue  169 GLN
Chi-restraints excluded: chain G residue  198 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
B 222 ASN
D   8 HIS
G 103 GLN
G 167 HIS
G 208 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.104200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.097412 restraints weight = 13669.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.096948 restraints weight = 18754.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.097503 restraints weight = 15738.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097174 restraints weight = 12501.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.097689 restraints weight = 10437.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      566 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1245 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6880  Z= 0.192
  Angle     :  0.739   8.622   9316  Z= 0.389
  Chirality :  0.048   0.152   1035
  Planarity :  0.005   0.052   1196
  Dihedral  :  6.252  54.297    936
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.40 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -3.57 (0.26), residues: 846
  helix:  None (None), residues: 0
  sheet: -2.17 (0.25), residues: 344
  loop : -2.58 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 215 
 TYR   0.019   0.002   TYR A 126 
 PHE   0.013   0.002   PHE G 159 
 TRP   0.006   0.001   TRP A 170 
 HIS   0.004   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6873)
  covalent geometry    : angle       0.73640 ( 9302)
  SS BOND              : bond        0.00892 (    7)
  SS BOND              : angle       1.83341 (   14)
  hydrogen bonds       : bond        0.03922 (  207)
  hydrogen bonds       : angle       6.32236 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   62 MET cc_start: 0.7810 (mtt) cc_final: 0.7546 (mtt)
REVERT: A  102 ASP cc_start: 0.8629 (p0) cc_final: 0.7787 (p0)
REVERT: A  158 ASP cc_start: 0.9229 (t70) cc_final: 0.8846 (t0)
REVERT: A  196 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8420 (p0)
REVERT: A  211 ASP cc_start: 0.9319 (p0) cc_final: 0.8570 (p0)
REVERT: B   61 ASP cc_start: 0.8953 (p0) cc_final: 0.8735 (p0)
REVERT: B  133 TYR cc_start: 0.8637 (p90) cc_final: 0.7854 (p90)
REVERT: B  180 ASP cc_start: 0.9020 (p0) cc_final: 0.8250 (p0)
REVERT: B  222 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8132 (p0)
REVERT: D   15 ILE cc_start: 0.7153 (mp) cc_final: 0.6153 (tp)
REVERT: D   33 TYR cc_start: 0.7092 (m-80) cc_final: 0.6676 (m-10)
REVERT: D   52 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8223 (mt-10)
REVERT: D   62 ASP cc_start: 0.8223 (p0) cc_final: 0.7535 (p0)
REVERT: D   76 VAL cc_start: 0.7235 (t) cc_final: 0.6796 (p)
REVERT: G   17 LYS cc_start: 0.9334 (mmtm) cc_final: 0.8903 (tttm)
REVERT: G   73 ARG cc_start: 0.9108 (ptm-80) cc_final: 0.8721 (ptm-80)
REVERT: G  121 ILE cc_start: 0.9080 (mm) cc_final: 0.8873 (tt)
  outliers start: 23
  outliers final: 12
  residues processed: 147
  average time/residue: 0.0793
  time to fit residues: 15.4937
Evaluate side-chains
  126 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain G residue  169 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0570
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.7102

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

Flipped N/Q/H residues before XYZ refinement:
B 222 ASN
B 228 GLN
G 147 GLN
G 169 GLN
G 180 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.087195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.082324 restraints weight = 14020.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.082461 restraints weight = 12114.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.082630 restraints weight = 10613.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.082964 restraints weight = 8437.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.083093 restraints weight = 6910.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1245 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1292 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   6880  Z= 0.218
  Angle     :  0.749   8.586   9316  Z= 0.393
  Chirality :  0.049   0.151   1035
  Planarity :  0.005   0.045   1196
  Dihedral  :  6.283  56.475    931
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 22.53 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -3.39 (0.26), residues: 846
  helix:  None (None), residues: 0
  sheet: -2.03 (0.25), residues: 356
  loop : -2.47 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  84 
 TYR   0.023   0.002   TYR A 126 
 PHE   0.014   0.002   PHE G 159 
 TRP   0.010   0.002   TRP G 196 
 HIS   0.003   0.001   HIS G 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 6873)
  covalent geometry    : angle       0.74647 ( 9302)
  SS BOND              : bond        0.01004 (    7)
  SS BOND              : angle       1.88502 (   14)
  hydrogen bonds       : bond        0.03933 (  207)
  hydrogen bonds       : angle       6.25161 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   62 MET cc_start: 0.7868 (mtt) cc_final: 0.7616 (mtt)
REVERT: A  102 ASP cc_start: 0.8625 (p0) cc_final: 0.7571 (p0)
REVERT: A  158 ASP cc_start: 0.9218 (t70) cc_final: 0.8979 (t70)
REVERT: A  211 ASP cc_start: 0.9284 (p0) cc_final: 0.8616 (p0)
REVERT: A  238 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7220 (mt-10)
REVERT: B  133 TYR cc_start: 0.8657 (p90) cc_final: 0.7926 (p90)
REVERT: B  180 ASP cc_start: 0.9006 (p0) cc_final: 0.8327 (p0)
REVERT: B  217 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8909 (mtt)
REVERT: B  222 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7967 (p0)
REVERT: D   15 ILE cc_start: 0.7615 (mp) cc_final: 0.6656 (tp)
REVERT: D   52 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8409 (mt-10)
REVERT: D   62 ASP cc_start: 0.7892 (p0) cc_final: 0.7293 (p0)
REVERT: D   76 VAL cc_start: 0.7606 (t) cc_final: 0.6998 (p)
REVERT: G   73 ARG cc_start: 0.9153 (ptm-80) cc_final: 0.8929 (ptm-80)
  outliers start: 38
  outliers final: 23
  residues processed: 146
  average time/residue: 0.0839
  time to fit residues: 16.2171
Evaluate side-chains
  137 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  209 ILE
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  178 VAL
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0000
   chunk 64 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN
B 222 ASN
B 228 GLN
G 167 HIS
G 208 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.088564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.084229 restraints weight = 14120.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.084685 restraints weight = 10038.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.085004 restraints weight = 7620.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.085103 restraints weight = 6444.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.085258 restraints weight = 5527.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1292 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1310 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6880  Z= 0.127
  Angle     :  0.667   8.546   9316  Z= 0.348
  Chirality :  0.047   0.148   1035
  Planarity :  0.005   0.043   1196
  Dihedral  :  5.260  19.736    928
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 24.53 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -3.00 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.72 (0.25), residues: 369
  loop : -2.23 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  85 
 TYR   0.013   0.001   TYR B 126 
 PHE   0.009   0.001   PHE B  76 
 TRP   0.008   0.001   TRP A 170 
 HIS   0.003   0.001   HIS D 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6873)
  covalent geometry    : angle       0.66612 ( 9302)
  SS BOND              : bond        0.00674 (    7)
  SS BOND              : angle       1.20015 (   14)
  hydrogen bonds       : bond        0.03187 (  207)
  hydrogen bonds       : angle       5.87456 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 127
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7787 (mtt) cc_final: 0.7520 (mtt)
REVERT: A  102 ASP cc_start: 0.8509 (p0) cc_final: 0.7772 (p0)
REVERT: A  211 ASP cc_start: 0.9295 (p0) cc_final: 0.8757 (p0)
REVERT: A  228 GLN cc_start: 0.8545 (mt0) cc_final: 0.8029 (mt0)
REVERT: A  233 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8771 (m)
REVERT: B   45 GLU cc_start: 0.9201 (mp0) cc_final: 0.8937 (tt0)
REVERT: B  125 CYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8959 (p)
REVERT: B  133 TYR cc_start: 0.8624 (p90) cc_final: 0.7908 (p90)
REVERT: B  134 ASP cc_start: 0.9272 (t0) cc_final: 0.8713 (t0)
REVERT: B  180 ASP cc_start: 0.8901 (p0) cc_final: 0.8278 (p0)
REVERT: B  217 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8875 (mtt)
REVERT: D   15 ILE cc_start: 0.7650 (mp) cc_final: 0.6789 (tp)
REVERT: D   62 ASP cc_start: 0.7775 (p0) cc_final: 0.7120 (p0)
REVERT: D   64 PHE cc_start: 0.7889 (m-80) cc_final: 0.7462 (m-80)
REVERT: D   76 VAL cc_start: 0.7429 (t) cc_final: 0.6832 (p)
REVERT: G   73 ARG cc_start: 0.9053 (ptm-80) cc_final: 0.8851 (ptt180)
  outliers start: 31
  outliers final: 18
  residues processed: 149
  average time/residue: 0.0831
  time to fit residues: 16.6012
Evaluate side-chains
  138 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0970
   overall best weight:    1.7582

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN
G 169 GLN
G 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.085111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.081155 restraints weight = 14449.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.081158 restraints weight = 17689.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.081733 restraints weight = 13173.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.081848 restraints weight = 8261.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.081963 restraints weight = 6803.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1310 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1314 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   6880  Z= 0.223
  Angle     :  0.752   8.564   9316  Z= 0.392
  Chirality :  0.048   0.189   1035
  Planarity :  0.005   0.048   1196
  Dihedral  :  5.519  20.660    928
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.81 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 26.00 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -3.06 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.69 (0.24), residues: 386
  loop : -2.34 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 168 
 TYR   0.025   0.002   TYR A 126 
 PHE   0.012   0.002   PHE G 159 
 TRP   0.008   0.002   TRP A 170 
 HIS   0.005   0.001   HIS G 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 6873)
  covalent geometry    : angle       0.74968 ( 9302)
  SS BOND              : bond        0.00982 (    7)
  SS BOND              : angle       1.62753 (   14)
  hydrogen bonds       : bond        0.03781 (  207)
  hydrogen bonds       : angle       6.04839 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7869 (mtt) cc_final: 0.7606 (mtt)
REVERT: A  102 ASP cc_start: 0.8595 (p0) cc_final: 0.7830 (p0)
REVERT: A  211 ASP cc_start: 0.9344 (p0) cc_final: 0.8853 (p0)
REVERT: A  228 GLN cc_start: 0.8628 (mt0) cc_final: 0.8172 (mt0)
REVERT: B   45 GLU cc_start: 0.9186 (mp0) cc_final: 0.8945 (tt0)
REVERT: B  180 ASP cc_start: 0.8919 (p0) cc_final: 0.8385 (p0)
REVERT: B  217 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8909 (mtt)
REVERT: D   15 ILE cc_start: 0.7647 (mp) cc_final: 0.6710 (tp)
REVERT: D   52 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8352 (mt-10)
REVERT: D   62 ASP cc_start: 0.7668 (p0) cc_final: 0.7040 (p0)
REVERT: D   64 PHE cc_start: 0.7900 (m-80) cc_final: 0.7450 (m-80)
REVERT: D   76 VAL cc_start: 0.7197 (t) cc_final: 0.6661 (p)
REVERT: D  150 ILE cc_start: 0.2047 (tt) cc_final: 0.1540 (tt)
REVERT: G   73 ARG cc_start: 0.9118 (ptm-80) cc_final: 0.8916 (ptm-80)
  outliers start: 34
  outliers final: 26
  residues processed: 144
  average time/residue: 0.0843
  time to fit residues: 16.1071
Evaluate side-chains
  144 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  169 GLN
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 68 optimal weight:    0.3980
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN
B 228 GLN
G 169 GLN
G 208 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.087270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.083687 restraints weight = 14355.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.083761 restraints weight = 16490.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.084358 restraints weight = 11429.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.084390 restraints weight = 7567.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.084577 restraints weight = 6344.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1314 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2949 r_free = 0.2949    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1356 |
|-----------------------------------------------------------------------------|
r_final: 0.2949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6880  Z= 0.148
  Angle     :  0.692   8.570   9316  Z= 0.360
  Chirality :  0.047   0.153   1035
  Planarity :  0.005   0.049   1196
  Dihedral  :  5.295  19.452    928
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 25.47 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -2.89 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.57 (0.24), residues: 387
  loop : -2.23 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 168 
 TYR   0.014   0.001   TYR A 126 
 PHE   0.008   0.001   PHE B 127 
 TRP   0.007   0.001   TRP G  37 
 HIS   0.007   0.001   HIS G 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6873)
  covalent geometry    : angle       0.69050 ( 9302)
  SS BOND              : bond        0.00745 (    7)
  SS BOND              : angle       1.37508 (   14)
  hydrogen bonds       : bond        0.03278 (  207)
  hydrogen bonds       : angle       5.82846 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8673 (mm)
REVERT: A   62 MET cc_start: 0.7779 (mtt) cc_final: 0.7534 (mtt)
REVERT: A  102 ASP cc_start: 0.8548 (p0) cc_final: 0.7578 (p0)
REVERT: A  211 ASP cc_start: 0.9310 (p0) cc_final: 0.8872 (p0)
REVERT: A  228 GLN cc_start: 0.8679 (mt0) cc_final: 0.8189 (mt0)
REVERT: A  233 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8741 (m)
REVERT: A  238 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7201 (mt-10)
REVERT: B   45 GLU cc_start: 0.9200 (mp0) cc_final: 0.8983 (tt0)
REVERT: B   61 ASP cc_start: 0.9014 (p0) cc_final: 0.8658 (p0)
REVERT: B  125 CYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8975 (p)
REVERT: B  133 TYR cc_start: 0.8597 (p90) cc_final: 0.7850 (p90)
REVERT: B  134 ASP cc_start: 0.9278 (t0) cc_final: 0.8705 (t0)
REVERT: B  180 ASP cc_start: 0.8848 (p0) cc_final: 0.8292 (p0)
REVERT: B  211 ASP cc_start: 0.8435 (p0) cc_final: 0.8095 (p0)
REVERT: B  217 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8900 (mtt)
REVERT: D   15 ILE cc_start: 0.7433 (mp) cc_final: 0.6311 (tp)
REVERT: D   62 ASP cc_start: 0.7617 (p0) cc_final: 0.6831 (p0)
REVERT: D   76 VAL cc_start: 0.7156 (t) cc_final: 0.6576 (p)
REVERT: D  150 ILE cc_start: 0.2233 (tt) cc_final: 0.1851 (tt)
REVERT: G   73 ARG cc_start: 0.9063 (ptm-80) cc_final: 0.8856 (ptt180)
  outliers start: 33
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0694
  time to fit residues: 13.8225
Evaluate side-chains
  149 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN
D  36 ASN
G 167 HIS
G 208 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.083478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.080128 restraints weight = 14324.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.080071 restraints weight = 15521.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.080705 restraints weight = 11973.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.080759 restraints weight = 7530.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.080806 restraints weight = 6461.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1356 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1347 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.099   6880  Z= 0.285
  Angle     :  0.816   9.715   9316  Z= 0.425
  Chirality :  0.049   0.179   1035
  Planarity :  0.006   0.051   1196
  Dihedral  :  5.798  21.592    928
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.58 %
    Favored  : 88.42 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.47 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -3.04 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.65 (0.25), residues: 380
  loop : -2.36 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  84 
 TYR   0.033   0.002   TYR A 126 
 PHE   0.016   0.002   PHE B  67 
 TRP   0.013   0.002   TRP G 196 
 HIS   0.006   0.001   HIS G 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 6873)
  covalent geometry    : angle       0.81282 ( 9302)
  SS BOND              : bond        0.01212 (    7)
  SS BOND              : angle       1.92990 (   14)
  hydrogen bonds       : bond        0.04242 (  207)
  hydrogen bonds       : angle       6.25558 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 111
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8739 (mm)
REVERT: A   83 GLU cc_start: 0.8155 (tt0) cc_final: 0.7849 (mt-10)
REVERT: A  102 ASP cc_start: 0.8656 (p0) cc_final: 0.8429 (p0)
REVERT: A  211 ASP cc_start: 0.9373 (p0) cc_final: 0.8990 (p0)
REVERT: A  228 GLN cc_start: 0.8824 (mt0) cc_final: 0.8330 (mt0)
REVERT: B   45 GLU cc_start: 0.9226 (mp0) cc_final: 0.8965 (tt0)
REVERT: B   61 ASP cc_start: 0.9001 (p0) cc_final: 0.8747 (p0)
REVERT: B  180 ASP cc_start: 0.8991 (p0) cc_final: 0.8502 (p0)
REVERT: B  211 ASP cc_start: 0.8700 (p0) cc_final: 0.8437 (p0)
REVERT: B  217 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8924 (mtt)
REVERT: D   15 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.6587 (tp)
REVERT: D   62 ASP cc_start: 0.7615 (p0) cc_final: 0.7044 (p0)
REVERT: D   64 PHE cc_start: 0.7978 (m-80) cc_final: 0.7340 (m-80)
REVERT: D   76 VAL cc_start: 0.7304 (t) cc_final: 0.6766 (p)
REVERT: D  150 ILE cc_start: 0.2445 (tt) cc_final: 0.1767 (tt)
REVERT: G   73 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8958 (ptt180)
  outliers start: 41
  outliers final: 33
  residues processed: 142
  average time/residue: 0.0773
  time to fit residues: 14.5720
Evaluate side-chains
  145 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   15 ILE
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain G residue   18 THR
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   45 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   64 ILE
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0770
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN
D  36 ASN
G 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.087666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.084211 restraints weight = 14116.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.084154 restraints weight = 15381.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.084716 restraints weight = 11842.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.084857 restraints weight = 8156.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.084896 restraints weight = 6740.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1347 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1364 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6880  Z= 0.136
  Angle     :  0.702   9.428   9316  Z= 0.364
  Chirality :  0.047   0.155   1035
  Planarity :  0.005   0.052   1196
  Dihedral  :  5.329  19.683    928
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 26.27 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -2.82 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.51 (0.24), residues: 387
  loop : -2.20 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 210 
 TYR   0.014   0.001   TYR B 126 
 PHE   0.009   0.001   PHE B  98 
 TRP   0.014   0.001   TRP G 168 
 HIS   0.006   0.001   HIS G 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6873)
  covalent geometry    : angle       0.70032 ( 9302)
  SS BOND              : bond        0.00687 (    7)
  SS BOND              : angle       1.26348 (   14)
  hydrogen bonds       : bond        0.03299 (  207)
  hydrogen bonds       : angle       5.83558 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7877 (mtt) cc_final: 0.7640 (mtt)
REVERT: A  102 ASP cc_start: 0.8565 (p0) cc_final: 0.7641 (p0)
REVERT: A  211 ASP cc_start: 0.9299 (p0) cc_final: 0.8924 (p0)
REVERT: A  228 GLN cc_start: 0.8697 (mt0) cc_final: 0.8206 (mt0)
REVERT: A  233 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8751 (m)
REVERT: B   45 GLU cc_start: 0.9208 (mp0) cc_final: 0.9000 (tt0)
REVERT: B   82 ARG cc_start: 0.7434 (ptt-90) cc_final: 0.7199 (ptt-90)
REVERT: B  125 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8983 (p)
REVERT: B  133 TYR cc_start: 0.8569 (p90) cc_final: 0.7781 (p90)
REVERT: B  134 ASP cc_start: 0.9243 (t0) cc_final: 0.8675 (t0)
REVERT: B  180 ASP cc_start: 0.8856 (p0) cc_final: 0.8342 (p0)
REVERT: B  211 ASP cc_start: 0.8460 (p0) cc_final: 0.8097 (p0)
REVERT: B  217 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8854 (mtt)
REVERT: D   15 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6349 (tp)
REVERT: D   33 TYR cc_start: 0.7410 (m-80) cc_final: 0.6582 (m-80)
REVERT: D   62 ASP cc_start: 0.7539 (p0) cc_final: 0.6851 (p0)
REVERT: D   64 PHE cc_start: 0.7905 (m-80) cc_final: 0.7312 (m-80)
REVERT: D   76 VAL cc_start: 0.7254 (t) cc_final: 0.6631 (p)
REVERT: D  150 ILE cc_start: 0.2314 (tt) cc_final: 0.1868 (tt)
  outliers start: 33
  outliers final: 28
  residues processed: 148
  average time/residue: 0.0651
  time to fit residues: 12.9665
Evaluate side-chains
  154 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   15 ILE
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  208 HIS
Chi-restraints excluded: chain G residue  215 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0370
   chunk 20 optimal weight:    0.4980
   overall best weight:    1.2862

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN
D  36 ASN
G 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.086374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.082816 restraints weight = 14270.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.082740 restraints weight = 16276.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.083228 restraints weight = 12236.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.083597 restraints weight = 8186.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.083627 restraints weight = 6518.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1364 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1366 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6880  Z= 0.180
  Angle     :  0.743  10.534   9316  Z= 0.384
  Chirality :  0.048   0.164   1035
  Planarity :  0.005   0.054   1196
  Dihedral  :  5.410  19.358    928
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.10 %
    Favored  : 90.90 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 25.87 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -2.81 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.48 (0.25), residues: 386
  loop : -2.21 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 168 
 TYR   0.019   0.002   TYR A 126 
 PHE   0.009   0.002   PHE G 159 
 TRP   0.011   0.002   TRP G 168 
 HIS   0.006   0.001   HIS G 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 6873)
  covalent geometry    : angle       0.74125 ( 9302)
  SS BOND              : bond        0.00876 (    7)
  SS BOND              : angle       1.50015 (   14)
  hydrogen bonds       : bond        0.03528 (  207)
  hydrogen bonds       : angle       5.88167 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 119
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8685 (mm)
REVERT: A   62 MET cc_start: 0.7879 (mtt) cc_final: 0.7641 (mtt)
REVERT: A   83 GLU cc_start: 0.7967 (tt0) cc_final: 0.7636 (mt-10)
REVERT: A  102 ASP cc_start: 0.8605 (p0) cc_final: 0.7741 (p0)
REVERT: A  211 ASP cc_start: 0.9319 (p0) cc_final: 0.8966 (p0)
REVERT: A  228 GLN cc_start: 0.8697 (mt0) cc_final: 0.8210 (mt0)
REVERT: B   82 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.6780 (ptt-90)
REVERT: B   84 ARG cc_start: 0.8039 (mmt90) cc_final: 0.7672 (mmt90)
REVERT: B  125 CYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8979 (p)
REVERT: B  133 TYR cc_start: 0.8583 (p90) cc_final: 0.7771 (p90)
REVERT: B  180 ASP cc_start: 0.8872 (p0) cc_final: 0.8371 (p0)
REVERT: B  211 ASP cc_start: 0.8510 (p0) cc_final: 0.8183 (p0)
REVERT: B  217 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8870 (mtt)
REVERT: D   15 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.6431 (tp)
REVERT: D   33 TYR cc_start: 0.7390 (m-80) cc_final: 0.6537 (m-80)
REVERT: D   62 ASP cc_start: 0.7535 (p0) cc_final: 0.6840 (p0)
REVERT: D   64 PHE cc_start: 0.7903 (m-80) cc_final: 0.7356 (m-80)
REVERT: D   76 VAL cc_start: 0.7275 (t) cc_final: 0.6645 (p)
REVERT: D  150 ILE cc_start: 0.2335 (tt) cc_final: 0.1861 (tt)
  outliers start: 39
  outliers final: 31
  residues processed: 148
  average time/residue: 0.0722
  time to fit residues: 14.3990
Evaluate side-chains
  152 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 117
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  214 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   15 ILE
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0370
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8064

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN
D  36 ASN
G 208 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.087798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.084309 restraints weight = 14155.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.084269 restraints weight = 15857.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.084890 restraints weight = 11844.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.085085 restraints weight = 7464.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.085209 restraints weight = 6481.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2962
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2962 r_free = 0.2962    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1366 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1365 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6880  Z= 0.146
  Angle     :  0.716  11.337   9316  Z= 0.371
  Chirality :  0.047   0.162   1035
  Planarity :  0.005   0.053   1196
  Dihedral  :  5.225  19.397    928
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 26.27 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -2.65 (0.27), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.34 (0.25), residues: 387
  loop : -2.15 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 168 
 TYR   0.013   0.001   TYR B 126 
 PHE   0.018   0.002   PHE B 240 
 TRP   0.013   0.001   TRP G 168 
 HIS   0.009   0.001   HIS G 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6873)
  covalent geometry    : angle       0.71452 ( 9302)
  SS BOND              : bond        0.00727 (    7)
  SS BOND              : angle       1.32199 (   14)
  hydrogen bonds       : bond        0.03259 (  207)
  hydrogen bonds       : angle       5.72281 (  522)

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8653 (mm)
REVERT: A  102 ASP cc_start: 0.8561 (p0) cc_final: 0.7654 (p0)
REVERT: A  211 ASP cc_start: 0.9292 (p0) cc_final: 0.8987 (p0)
REVERT: A  228 GLN cc_start: 0.8687 (mt0) cc_final: 0.8182 (mt0)
REVERT: B  125 CYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8961 (p)
REVERT: B  133 TYR cc_start: 0.8572 (p90) cc_final: 0.7799 (p90)
REVERT: B  134 ASP cc_start: 0.9268 (t0) cc_final: 0.8674 (t0)
REVERT: B  180 ASP cc_start: 0.8823 (p0) cc_final: 0.8294 (p0)
REVERT: B  211 ASP cc_start: 0.8470 (p0) cc_final: 0.8126 (p0)
REVERT: B  217 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8867 (mtt)
REVERT: B  231 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8293 (mt-10)
REVERT: D   15 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6326 (tp)
REVERT: D   33 TYR cc_start: 0.7437 (m-80) cc_final: 0.6598 (m-80)
REVERT: D   62 ASP cc_start: 0.7407 (p0) cc_final: 0.6749 (p0)
REVERT: D   64 PHE cc_start: 0.7813 (m-80) cc_final: 0.7251 (m-80)
REVERT: D   76 VAL cc_start: 0.7168 (t) cc_final: 0.6555 (p)
REVERT: D  150 ILE cc_start: 0.2258 (tt) cc_final: 0.1605 (tt)
REVERT: G    8 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6810 (mm-40)
  outliers start: 36
  outliers final: 30
  residues processed: 152
  average time/residue: 0.0647
  time to fit residues: 13.1299
Evaluate side-chains
  159 residues out of total 750 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 124
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  115 ILE
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue   86 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  125 CYS
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  166 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 GLN
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   15 ILE
Chi-restraints excluded: chain D residue   60 PHE
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain G residue    8 GLN
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   50 VAL
Chi-restraints excluded: chain G residue   77 THR
Chi-restraints excluded: chain G residue   81 THR
Chi-restraints excluded: chain G residue  157 GLU
Chi-restraints excluded: chain G residue  169 GLN
Chi-restraints excluded: chain G residue  208 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 28 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 228 GLN
D  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.088201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.084739 restraints weight = 14082.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.084775 restraints weight = 14600.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.085299 restraints weight = 10850.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.085453 restraints weight = 7331.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.085502 restraints weight = 6401.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2966 r_free = 0.2966    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1365 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1387 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6880  Z= 0.147
  Angle     :  0.722  11.573   9316  Z= 0.373
  Chirality :  0.047   0.201   1035
  Planarity :  0.005   0.050   1196
  Dihedral  :  5.189  19.326    928
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 26.40 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.78 %
    Cis-general     : 1.61 %
    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: -2.56 (0.28), residues: 846
  helix:  None (None), residues: 0
  sheet: -1.28 (0.24), residues: 389
  loop : -2.07 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 168 
 TYR   0.013   0.001   TYR B 126 
 PHE   0.033   0.002   PHE B 240 
 TRP   0.012   0.001   TRP G 168 
 HIS   0.003   0.001   HIS D 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6873)
  covalent geometry    : angle       0.72047 ( 9302)
  SS BOND              : bond        0.00722 (    7)
  SS BOND              : angle       1.30938 (   14)
  hydrogen bonds       : bond        0.03271 (  207)
  hydrogen bonds       : angle       5.65882 (  522)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1188.55 seconds
wall clock time: 21 minutes 5.15 seconds (1265.15 seconds total)