Starting phenix.real_space_refine
on Fri Oct 10 12:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t05_40935/10_2025/8t05_40935.cif"
  }
  resolution = 3.22
  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=   0.004 sd=   0.066
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P       2      5.49       5
     S      22      5.16       5
     C    3387      2.51       5
     N     798      2.21       5
     O     893      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5104
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 7, 'TRANS': 193}
    Chain: "B"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 7, 'TRANS': 193}
    Chain: "C"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "D"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 831
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 72
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 72
          Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 2
  Time building chain proxies: 1.42, per 1000 atoms: 0.28
  Number of scatterers: 5104
  At special positions: 0
  Unit cell: (81.34, 88.81, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      22     16.00
     P       2     15.00
     O     893      8.00
     N     798      7.00
     C    3387      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  60 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.05

  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: 0.32
  Conformation dependent library (CDL) restraints added in 193.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 301 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 182 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A 186 "
        pdb="ZN    ZN A 301 " - pdb=" NE2 HIS A  48 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  48 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 186 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B 182 "


  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1158

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 4 sheets defined
      55.6% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 14
      removed outlier: 3.844A  pdb=" N   VAL A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 15 through 17
      No H-bonds generated for 'chain 'A' and resid 15 through 17'
    Processing helix  chain 'A' and resid 18 through 28
      removed outlier: 3.546A  pdb=" N   GLY A  22 " --> pdb=" O   PHE A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 51
      removed outlier: 4.083A  pdb=" N   LEU A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 63
      removed outlier: 3.692A  pdb=" N   MET A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 86
      removed outlier: 3.738A  pdb=" N   THR A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 112
      removed outlier: 3.555A  pdb=" N   GLU A 112 " --> pdb=" O   ARG A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 142
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 154 through 171
    Processing helix  chain 'A' and resid 177 through 198
      removed outlier: 3.787A  pdb=" N   SER A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG A 198 " --> pdb=" O   THR A 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 14
      Proline residue:  B  11  - end of helix
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 18 through 28
      removed outlier: 3.721A  pdb=" N   GLY B  22 " --> pdb=" O   PHE B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 52
    Processing helix  chain 'B' and resid 63 through 86
      removed outlier: 3.628A  pdb=" N   PHE B  69 " --> pdb=" O   LYS B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 112
    Processing helix  chain 'B' and resid 119 through 141
    Processing helix  chain 'B' and resid 147 through 153
    Processing helix  chain 'B' and resid 154 through 171
    Processing helix  chain 'B' and resid 177 through 197
      removed outlier: 3.965A  pdb=" N   SER B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.885A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11
      removed outlier: 5.688A  pdb=" N   GLU C  10 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 118 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   MET C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ALA C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.072A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24
      removed outlier: 3.533A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    864 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: 0.75

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 746
        1.31 -     1.44: 1499
        1.44 -     1.56: 2946
        1.56 -     1.69: 14
        1.69 -     1.82: 32
  Bond restraints: 5237
  Sorted by residual:
  bond pdb=" C   GLY C   8 "
       pdb=" N   ALA C   9 "
    ideal  model  delta    sigma   weight residual
    1.331  1.409 -0.077 1.30e-02 5.92e+03 3.53e+01
  bond pdb=" C25 LBN A 303 "
       pdb=" O5  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.433 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C25 LBN B 303 "
       pdb=" O5  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.326  1.429 -0.103 2.00e-02 2.50e+03 2.65e+01
  bond pdb=" C34 LBN A 303 "
       pdb=" O7  LBN A 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.427 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C34 LBN B 303 "
       pdb=" O7  LBN B 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.424 -0.093 2.00e-02 2.50e+03 2.16e+01
  ... (remaining 5232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.92: 6281
        2.92 -     5.84: 805
        5.84 -     8.76: 12
        8.76 -    11.68: 5
       11.68 -    14.60: 2
  Bond angle restraints: 7105
  Sorted by residual:
  angle pdb=" N   PHE C 109 "
        pdb=" CA  PHE C 109 "
        pdb=" C   PHE C 109 "
      ideal   model   delta    sigma   weight residual
     111.24  118.85   -7.61 1.38e+00 5.25e-01 3.04e+01
  angle pdb=" C   GLY A 101 "
        pdb=" N   GLY A 102 "
        pdb=" CA  GLY A 102 "
      ideal   model   delta    sigma   weight residual
     120.03  125.59   -5.56 1.12e+00 7.97e-01 2.47e+01
  angle pdb=" N   THR D  94 "
        pdb=" CA  THR D  94 "
        pdb=" C   THR D  94 "
      ideal   model   delta    sigma   weight residual
     108.82  117.00   -8.18 1.65e+00 3.67e-01 2.46e+01
  angle pdb=" O1  LBN B 303 "
        pdb=" P1  LBN B 303 "
        pdb=" O2  LBN B 303 "
      ideal   model   delta    sigma   weight residual
      93.45  108.05  -14.60 3.00e+00 1.11e-01 2.37e+01
  angle pdb=" O1  LBN A 303 "
        pdb=" P1  LBN A 303 "
        pdb=" O2  LBN A 303 "
      ideal   model   delta    sigma   weight residual
      93.45  107.88  -14.43 3.00e+00 1.11e-01 2.31e+01
  ... (remaining 7100 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.48: 3038
       30.48 -    60.96: 92
       60.96 -    91.44: 11
       91.44 -   121.92: 7
      121.92 -   152.40: 4
  Dihedral angle restraints: 3152
    sinusoidal: 1337
      harmonic: 1815
  Sorted by residual:
  dihedral pdb=" CA  THR D  94 "
           pdb=" C   THR D  94 "
           pdb=" N   PRO D  95 "
           pdb=" CA  PRO D  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   70.79  109.21     0      5.00e+00 4.00e-02 4.77e+02
  dihedral pdb=" CA  ALA D  50 "
           pdb=" C   ALA D  50 "
           pdb=" N   ALA D  51 "
           pdb=" CA  ALA D  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.52  -28.48     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  SER B  56 "
           pdb=" C   SER B  56 "
           pdb=" N   LEU B  57 "
           pdb=" CA  LEU B  57 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.12  -24.88     0      5.00e+00 4.00e-02 2.48e+01
  ... (remaining 3149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.985: 803
       0.985 -    1.969: 0
       1.969 -    2.954: 0
       2.954 -    3.938: 0
       3.938 -    4.923: 2
  Chirality restraints: 805
  Sorted by residual:
  chirality pdb=" C2  LBN B 303 "
            pdb=" C1  LBN B 303 "
            pdb=" C3  LBN B 303 "
            pdb=" O7  LBN B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.56   -4.92 2.00e-01 2.50e+01 6.06e+02
  chirality pdb=" C2  LBN A 303 "
            pdb=" C1  LBN A 303 "
            pdb=" C3  LBN A 303 "
            pdb=" O7  LBN A 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36    2.55   -4.92 2.00e-01 2.50e+01 6.04e+02
  chirality pdb=" C14 CLR A 302 "
            pdb=" C13 CLR A 302 "
            pdb=" C15 CLR A 302 "
            pdb=" C8  CLR A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.40 2.00e-01 2.50e+01 3.97e+00
  ... (remaining 802 not shown)

  Planarity restraints: 848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 145 "   -0.060 5.00e-02 4.00e+02   9.05e-02 1.31e+01
        pdb=" N   PRO B 146 "    0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C  13 "   -0.054 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO C  14 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  94 "   -0.042 5.00e-02 4.00e+02   6.45e-02 6.65e+00
        pdb=" N   PRO D  95 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D  95 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D  95 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 845 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 71
        2.68 -     3.23: 4609
        3.23 -     3.79: 7701
        3.79 -     4.34: 10686
        4.34 -     4.90: 18018
  Nonbonded interactions: 41085
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A  44 "
            pdb="ZN    ZN A 301 "
     model   vdw
     2.120 2.230
  nonbonded pdb=" OE1 GLN B  44 "
            pdb="ZN    ZN B 301 "
     model   vdw
     2.172 2.230
  nonbonded pdb=" NH2 ARG D  61 "
            pdb=" OE2 GLU D  81 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" NH2 ARG A 108 "
            pdb=" O   PRO A 116 "
     model   vdw
     2.413 3.120
  nonbonded pdb=" O   HIS D  90 "
            pdb=" ND1 HIS D  90 "
     model   vdw
     2.433 3.120
  ... (remaining 41080 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain '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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.900
  Find NCS groups from input model:        0.050
  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:   10.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
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      :  0.015   0.181   5247  Z= 1.079
  Angle     :  1.851  14.605   7113  Z= 1.349
  Chirality :  0.259   4.923    805
  Planarity :  0.006   0.091    848
  Dihedral  : 16.958 152.400   1982
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.94 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  6.16 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.31), residues: 623
  helix: -1.21 (0.25), residues: 313
  sheet: -1.44 (0.49), residues: 86
  loop : -1.32 (0.44), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 108 
 TYR   0.043   0.003   TYR D  49 
 PHE   0.019   0.002   PHE B  43 
 TRP   0.027   0.003   TRP A 151 
 HIS   0.007   0.002   HIS D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.01446 ( 5237)
  covalent geometry    : angle       1.85126 ( 7105)
  SS BOND              : bond        0.01077 (    4)
  SS BOND              : angle       1.19535 (    8)
  hydrogen bonds       : bond        0.19464 (  298)
  hydrogen bonds       : angle       9.16980 (  864)
  metal coordination   : bond        0.11605 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30)
REVERT: A  198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80)
REVERT: B   62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm)
REVERT: B  184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt)
REVERT: C   10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0)
REVERT: C   28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t)
REVERT: C   32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80)
REVERT: C   34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt)
REVERT: D   30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80)
REVERT: D   71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80)
REVERT: D  100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30)
  outliers start: 5
  outliers final: 4
  residues processed: 92
  average time/residue: 0.1004
  time to fit residues: 11.3644
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 PRO
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain D residue   90 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B 113 ASN
B 186 HIS
D   6 GLN
D  28 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.171548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.139700 restraints weight = 6003.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 2.19
r_work: 0.3610 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.234   5247  Z= 0.188
  Angle     :  0.644   7.858   7113  Z= 0.333
  Chirality :  0.042   0.190    805
  Planarity :  0.005   0.077    848
  Dihedral  : 16.720 148.206    890
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.19 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.34), residues: 623
  helix:  1.27 (0.28), residues: 310
  sheet: -1.08 (0.45), residues: 125
  loop : -0.74 (0.50), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 140 
 TYR   0.013   0.001   TYR B  37 
 PHE   0.016   0.002   PHE B  43 
 TRP   0.022   0.002   TRP C  47 
 HIS   0.006   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5237)
  covalent geometry    : angle       0.64303 ( 7105)
  SS BOND              : bond        0.00224 (    4)
  SS BOND              : angle       1.01174 (    8)
  hydrogen bonds       : bond        0.04505 (  298)
  hydrogen bonds       : angle       4.98120 (  864)
  metal coordination   : bond        0.09546 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  112 GLU cc_start: 0.7442 (tt0) cc_final: 0.7228 (tt0)
REVERT: A  137 GLU cc_start: 0.7890 (tp30) cc_final: 0.7293 (mm-30)
REVERT: B   62 MET cc_start: 0.6944 (mtt) cc_final: 0.6740 (mtm)
REVERT: B  184 ILE cc_start: 0.8284 (mm) cc_final: 0.7956 (mt)
REVERT: B  198 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8394 (mtp85)
REVERT: D   30 TYR cc_start: 0.8913 (m-80) cc_final: 0.8563 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 93
  average time/residue: 0.0959
  time to fit residues: 11.0281
Evaluate side-chains
  82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain C residue   88 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
B  95 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.173134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141518 restraints weight = 5909.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 2.17
r_work: 0.3631 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5247  Z= 0.134
  Angle     :  0.576   6.612   7113  Z= 0.292
  Chirality :  0.040   0.194    805
  Planarity :  0.005   0.078    848
  Dihedral  : 14.657 141.947    881
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.06 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.36), residues: 623
  helix:  2.09 (0.29), residues: 313
  sheet: -0.81 (0.49), residues: 110
  loop : -0.78 (0.50), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 140 
 TYR   0.013   0.001   TYR D  49 
 PHE   0.015   0.001   PHE B  70 
 TRP   0.017   0.001   TRP C  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5237)
  covalent geometry    : angle       0.57532 ( 7105)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       0.95402 (    8)
  hydrogen bonds       : bond        0.04025 (  298)
  hydrogen bonds       : angle       4.39518 (  864)
  metal coordination   : bond        0.00636 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8141 (tptt)
REVERT: A   88 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7811 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7865 (tp30) cc_final: 0.7254 (mm-30)
REVERT: B   27 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8030 (ttpt)
REVERT: C    5 GLN cc_start: 0.8179 (tt0) cc_final: 0.7933 (tt0)
REVERT: C   90 ASP cc_start: 0.8712 (m-30) cc_final: 0.8499 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0948
  time to fit residues: 9.7861
Evaluate side-chains
  82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.174263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.141951 restraints weight = 6003.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.19
r_work: 0.3631 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5247  Z= 0.147
  Angle     :  0.578   6.185   7113  Z= 0.293
  Chirality :  0.041   0.195    805
  Planarity :  0.005   0.078    848
  Dihedral  : 12.923 145.676    881
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.25 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.36), residues: 623
  helix:  2.28 (0.29), residues: 306
  sheet: -0.85 (0.47), residues: 122
  loop : -0.55 (0.52), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 198 
 TYR   0.013   0.001   TYR D  49 
 PHE   0.017   0.001   PHE D  91 
 TRP   0.015   0.001   TRP C  47 
 HIS   0.005   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5237)
  covalent geometry    : angle       0.57602 ( 7105)
  SS BOND              : bond        0.00249 (    4)
  SS BOND              : angle       1.58644 (    8)
  hydrogen bonds       : bond        0.04097 (  298)
  hydrogen bonds       : angle       4.33273 (  864)
  metal coordination   : bond        0.00235 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8125 (tptt)
REVERT: A   88 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7796 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7887 (tp30) cc_final: 0.7217 (mm-30)
REVERT: B   27 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8005 (ttpt)
REVERT: B  138 MET cc_start: 0.7862 (mtp) cc_final: 0.7638 (mtp)
REVERT: C    5 GLN cc_start: 0.8189 (tt0) cc_final: 0.7939 (tt0)
REVERT: C   90 ASP cc_start: 0.8797 (m-30) cc_final: 0.8542 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0805
  time to fit residues: 7.8522
Evaluate side-chains
  81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   97 THR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0040
   chunk 56 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.177565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.146250 restraints weight = 6025.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.15
r_work: 0.3557 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.820   5247  Z= 0.395
  Angle     :  0.525   6.089   7113  Z= 0.265
  Chirality :  0.039   0.193    805
  Planarity :  0.005   0.077    848
  Dihedral  : 11.616 136.301    881
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.49 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.36), residues: 623
  helix:  2.48 (0.29), residues: 315
  sheet: -0.63 (0.49), residues: 108
  loop : -0.86 (0.49), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  13 
 TYR   0.012   0.001   TYR D  49 
 PHE   0.014   0.001   PHE B  70 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5237)
  covalent geometry    : angle       0.52316 ( 7105)
  SS BOND              : bond        0.00256 (    4)
  SS BOND              : angle       1.31430 (    8)
  hydrogen bonds       : bond        0.03751 (  298)
  hydrogen bonds       : angle       4.12040 (  864)
  metal coordination   : bond        0.33495 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8130 (tptt)
REVERT: A   88 ARG cc_start: 0.8031 (mtp-110) cc_final: 0.7790 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7793 (tp30) cc_final: 0.7120 (mm-30)
REVERT: B   27 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7926 (ttpt)
REVERT: B   62 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6863 (ttm)
REVERT: B  138 MET cc_start: 0.7853 (mtp) cc_final: 0.7646 (mtp)
REVERT: C    5 GLN cc_start: 0.8087 (tt0) cc_final: 0.7845 (tt0)
REVERT: C   90 ASP cc_start: 0.8715 (m-30) cc_final: 0.8457 (m-30)
REVERT: D  100 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8009 (mm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0874
  time to fit residues: 8.6201
Evaluate side-chains
  76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   62 MET
Chi-restraints excluded: chain C residue  119 THR
Chi-restraints excluded: chain D residue  106 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.175335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.143078 restraints weight = 6032.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 2.23
r_work: 0.3641 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.901   5247  Z= 0.439
  Angle     :  0.553   6.295   7113  Z= 0.279
  Chirality :  0.040   0.197    805
  Planarity :  0.005   0.079    848
  Dihedral  : 11.456 144.605    881
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.74 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.36), residues: 623
  helix:  2.45 (0.29), residues: 308
  sheet: -0.88 (0.47), residues: 122
  loop : -0.66 (0.51), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  13 
 TYR   0.015   0.001   TYR D  49 
 PHE   0.015   0.001   PHE D  91 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 5237)
  covalent geometry    : angle       0.55137 ( 7105)
  SS BOND              : bond        0.00228 (    4)
  SS BOND              : angle       1.31737 (    8)
  hydrogen bonds       : bond        0.03906 (  298)
  hydrogen bonds       : angle       4.18911 (  864)
  metal coordination   : bond        0.36781 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8678 (tmmt) cc_final: 0.8115 (tptt)
REVERT: A   88 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7794 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7832 (tp30) cc_final: 0.7028 (mm-30)
REVERT: B   27 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7980 (ttpt)
REVERT: B   62 MET cc_start: 0.7158 (ttm) cc_final: 0.6906 (ttm)
REVERT: B  138 MET cc_start: 0.7881 (mtp) cc_final: 0.7668 (mtp)
REVERT: C    5 GLN cc_start: 0.8115 (tt0) cc_final: 0.7870 (tt0)
REVERT: C   90 ASP cc_start: 0.8837 (m-30) cc_final: 0.8549 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0818
  time to fit residues: 8.0659
Evaluate side-chains
  77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.173860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.141777 restraints weight = 6070.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.22
r_work: 0.3627 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.848   5247  Z= 0.415
  Angle     :  0.547   6.246   7113  Z= 0.275
  Chirality :  0.040   0.197    805
  Planarity :  0.005   0.079    848
  Dihedral  : 10.727 149.889    881
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.11 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.36), residues: 623
  helix:  2.44 (0.29), residues: 308
  sheet: -0.86 (0.47), residues: 122
  loop : -0.72 (0.51), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  13 
 TYR   0.014   0.001   TYR D  49 
 PHE   0.014   0.001   PHE B  70 
 TRP   0.013   0.001   TRP C  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5237)
  covalent geometry    : angle       0.54538 ( 7105)
  SS BOND              : bond        0.00260 (    4)
  SS BOND              : angle       1.25868 (    8)
  hydrogen bonds       : bond        0.03916 (  298)
  hydrogen bonds       : angle       4.18663 (  864)
  metal coordination   : bond        0.34614 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8119 (tptt)
REVERT: A   88 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7813 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7844 (tp30) cc_final: 0.7035 (mm-30)
REVERT: B   27 LYS cc_start: 0.8324 (mmmt) cc_final: 0.7970 (ttpt)
REVERT: B   62 MET cc_start: 0.7131 (ttm) cc_final: 0.6894 (ttm)
REVERT: B  138 MET cc_start: 0.7886 (mtp) cc_final: 0.7673 (mtp)
REVERT: C    5 GLN cc_start: 0.8127 (tt0) cc_final: 0.7895 (tt0)
REVERT: C   90 ASP cc_start: 0.8848 (m-30) cc_final: 0.8559 (m-30)
REVERT: D   30 TYR cc_start: 0.8915 (m-80) cc_final: 0.8630 (m-10)
REVERT: D   74 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8147 (ptmm)
  outliers start: 9
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0793
  time to fit residues: 7.6794
Evaluate side-chains
  80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 56 optimal weight:    0.2980
   chunk 20 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.176336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.143818 restraints weight = 6059.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.36
r_work: 0.3652 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.917   5247  Z= 0.439
  Angle     :  0.524   6.155   7113  Z= 0.263
  Chirality :  0.039   0.194    805
  Planarity :  0.005   0.078    848
  Dihedral  : 10.350 149.913    881
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.49 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.36), residues: 623
  helix:  2.52 (0.29), residues: 315
  sheet: -0.83 (0.47), residues: 122
  loop : -0.83 (0.51), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  13 
 TYR   0.012   0.001   TYR D  49 
 PHE   0.013   0.001   PHE B  70 
 TRP   0.011   0.001   TRP C  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5237)
  covalent geometry    : angle       0.52283 ( 7105)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       1.23316 (    8)
  hydrogen bonds       : bond        0.03747 (  298)
  hydrogen bonds       : angle       4.08828 (  864)
  metal coordination   : bond        0.37436 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8142 (tptt)
REVERT: A   88 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7826 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7800 (tp30) cc_final: 0.7018 (mm-30)
REVERT: B   27 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8009 (ttpt)
REVERT: B  138 MET cc_start: 0.7972 (mtp) cc_final: 0.7760 (mtp)
REVERT: C   90 ASP cc_start: 0.8828 (m-30) cc_final: 0.8554 (m-30)
REVERT: D   74 LYS cc_start: 0.8591 (ptmm) cc_final: 0.8202 (ptmm)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0935
  time to fit residues: 9.0285
Evaluate side-chains
  80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.174588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.142639 restraints weight = 6055.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.23
r_work: 0.3644 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5247  Z= 0.132
  Angle     :  0.538   6.701   7113  Z= 0.269
  Chirality :  0.040   0.194    805
  Planarity :  0.005   0.077    848
  Dihedral  : 10.300 153.280    881
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.49 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.36), residues: 623
  helix:  2.52 (0.29), residues: 309
  sheet: -0.74 (0.47), residues: 122
  loop : -0.84 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  13 
 TYR   0.013   0.001   TYR D  49 
 PHE   0.013   0.001   PHE A  39 
 TRP   0.011   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5237)
  covalent geometry    : angle       0.53646 ( 7105)
  SS BOND              : bond        0.00209 (    4)
  SS BOND              : angle       1.23351 (    8)
  hydrogen bonds       : bond        0.03799 (  298)
  hydrogen bonds       : angle       4.10579 (  864)
  metal coordination   : bond        0.00632 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8132 (tptt)
REVERT: A   88 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7857 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7807 (tp30) cc_final: 0.7032 (mm-30)
REVERT: B   27 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7997 (ttpt)
REVERT: B  138 MET cc_start: 0.8009 (mtp) cc_final: 0.7777 (mtt)
REVERT: C   32 TYR cc_start: 0.8066 (m-80) cc_final: 0.7846 (m-10)
REVERT: C   90 ASP cc_start: 0.8841 (m-30) cc_final: 0.8555 (m-30)
REVERT: D   74 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8197 (ptmm)
  outliers start: 9
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0811
  time to fit residues: 7.7073
Evaluate side-chains
  77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.174421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.142442 restraints weight = 6127.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.24
r_work: 0.3513 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.839   5247  Z= 0.411
  Angle     :  0.548   7.190   7113  Z= 0.275
  Chirality :  0.040   0.193    805
  Planarity :  0.005   0.077    848
  Dihedral  : 10.365 160.695    881
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.49 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.36), residues: 623
  helix:  2.49 (0.29), residues: 308
  sheet: -0.74 (0.48), residues: 122
  loop : -0.69 (0.50), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  13 
 TYR   0.014   0.001   TYR D  49 
 PHE   0.014   0.001   PHE D  91 
 TRP   0.012   0.001   TRP C  47 
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5237)
  covalent geometry    : angle       0.54668 ( 7105)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       1.33536 (    8)
  hydrogen bonds       : bond        0.03873 (  298)
  hydrogen bonds       : angle       4.13751 (  864)
  metal coordination   : bond        0.34245 (    6)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LYS cc_start: 0.8669 (tmmt) cc_final: 0.8096 (tptt)
REVERT: A   88 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7837 (mmm-85)
REVERT: A  137 GLU cc_start: 0.7816 (tp30) cc_final: 0.7003 (mm-30)
REVERT: B   27 LYS cc_start: 0.8300 (mmmt) cc_final: 0.7917 (ttpt)
REVERT: B  138 MET cc_start: 0.7949 (mtp) cc_final: 0.7720 (mtt)
REVERT: C   32 TYR cc_start: 0.8065 (m-80) cc_final: 0.7805 (m-10)
REVERT: D   30 TYR cc_start: 0.8926 (m-80) cc_final: 0.8657 (m-10)
  outliers start: 9
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0947
  time to fit residues: 8.9617
Evaluate side-chains
  79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   88 SER
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0020
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 182 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.176948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145569 restraints weight = 6057.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 2.27
r_work: 0.3665 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.910   5247  Z= 0.435
  Angle     :  0.527   7.170   7113  Z= 0.264
  Chirality :  0.039   0.191    805
  Planarity :  0.005   0.075    848
  Dihedral  : 10.218 161.414    881
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.86 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.55 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.36), residues: 623
  helix:  2.64 (0.29), residues: 308
  sheet: -0.37 (0.51), residues: 108
  loop : -0.88 (0.47), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  13 
 TYR   0.013   0.001   TYR D  49 
 PHE   0.013   0.001   PHE A  39 
 TRP   0.011   0.001   TRP C  47 
 HIS   0.003   0.001   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5237)
  covalent geometry    : angle       0.52564 ( 7105)
  SS BOND              : bond        0.00201 (    4)
  SS BOND              : angle       1.09118 (    8)
  hydrogen bonds       : bond        0.03718 (  298)
  hydrogen bonds       : angle       4.06104 (  864)
  metal coordination   : bond        0.37159 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1308.28 seconds
wall clock time: 23 minutes 12.82 seconds (1392.82 seconds total)