Starting phenix.real_space_refine
on Tue Aug  4 22:53:36 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iu0_35713/08_2026/8iu0_35713.map"
  }
  resolution = 2.66
  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=   0.125
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      60      5.16       5
     C    4863      2.51       5
     N     954      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7062
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2102
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 255, 2072
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
      Conformer: "B"
        Number of residues, atoms: 255, 2072
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
          bond proxies already assigned to first conformer: 2117
    Chain: "A"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 252
          Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1}
          Classifications: {'undetermined': 15, 'water': 26}
          Link IDs: {None: 40}
          Unresolved non-hydrogen bonds: 387
          Unresolved non-hydrogen angles: 463
          Unresolved non-hydrogen dihedrals: 303
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-3': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4, 'PSC:plan-1': 6, 'PSC:plan-2': 6}
          Unresolved non-hydrogen planarities: 109
    Chain: "B"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 26
          Classifications: {'water': 26}
          Link IDs: {None: 25}
    Chain: "C"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 26
          Classifications: {'water': 26}
          Link IDs: {None: 25}
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  APHE A  35 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A  35 " occ=0.50
    residue:
      pdb=" N  APHE A 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 144 " occ=0.50
    residue:
      pdb=" N  APHE B  35 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B  35 " occ=0.50
    residue:
      pdb=" N  APHE B 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 144 " occ=0.50
    residue:
      pdb=" N  APHE C  35 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C  35 " occ=0.50
    residue:
      pdb=" N  APHE C 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 144 " occ=0.50
  Time building chain proxies: 1.67, per 1000 atoms: 0.24
  Number of scatterers: 7062
  At special positions: 0
  Unit cell: (77.19, 77.19, 84.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       9     15.00
     O    1176      8.00
     N     954      7.00
     C    4863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 577.5 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      74.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 48
    Processing helix  chain 'A' and resid 65 through 67
      No H-bonds generated for 'chain 'A' and resid 65 through 67'
    Processing helix  chain 'A' and resid 68 through 90
    Processing helix  chain 'A' and resid 105 through 122
      removed outlier: 3.644A  pdb=" N   THR A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 125 through 146
    Processing helix  chain 'A' and resid 149 through 177
      removed outlier: 3.781A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
    Processing helix  chain 'A' and resid 181 through 199
      removed outlier: 4.122A  pdb=" N   TRP A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 209
      removed outlier: 3.670A  pdb=" N   ILE A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
    Processing helix  chain 'A' and resid 233 through 252
    Processing helix  chain 'B' and resid 21 through 48
    Processing helix  chain 'B' and resid 65 through 67
      No H-bonds generated for 'chain 'B' and resid 65 through 67'
    Processing helix  chain 'B' and resid 68 through 90
    Processing helix  chain 'B' and resid 105 through 122
      removed outlier: 3.644A  pdb=" N   THR B 109 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 125 through 146
    Processing helix  chain 'B' and resid 149 through 177
      removed outlier: 3.781A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
    Processing helix  chain 'B' and resid 181 through 199
      removed outlier: 4.122A  pdb=" N   TRP B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 209
      removed outlier: 3.670A  pdb=" N   ILE B 207 " --> pdb=" O   PRO B 203 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
    Processing helix  chain 'B' and resid 233 through 252
    Processing helix  chain 'C' and resid 21 through 48
    Processing helix  chain 'C' and resid 65 through 67
      No H-bonds generated for 'chain 'C' and resid 65 through 67'
    Processing helix  chain 'C' and resid 68 through 90
    Processing helix  chain 'C' and resid 105 through 122
      removed outlier: 3.644A  pdb=" N   THR C 109 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
      Proline residue:  C 111  - end of helix
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'C' and resid 149 through 177
      removed outlier: 3.781A  pdb=" N   ALA C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 164  - end of helix
    Processing helix  chain 'C' and resid 181 through 199
      removed outlier: 4.122A  pdb=" N   TRP C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 209
      removed outlier: 3.670A  pdb=" N   ILE C 207 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE C 208 " --> pdb=" O   ILE C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 233
    Processing helix  chain 'C' and resid 233 through 252

    426 hydrogen bonds defined for protein.
    1281 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: 1.13

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1226
        1.33 -     1.46: 2621
        1.46 -     1.59: 3260
        1.59 -     1.72: 15
        1.72 -     1.85: 81
  Bond restraints: 7203
  Sorted by residual:
  bond pdb=" C7  PSC C 310 "
       pdb=" C8  PSC C 310 "
    ideal  model  delta    sigma   weight residual
    1.530  1.319  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C3  PSC A 311 "
       pdb=" C4  PSC A 311 "
    ideal  model  delta    sigma   weight residual
    1.524  1.313  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C3  PSC B 311 "
       pdb=" C4  PSC B 311 "
    ideal  model  delta    sigma   weight residual
    1.524  1.313  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C3  PSC C 311 "
       pdb=" C4  PSC C 311 "
    ideal  model  delta    sigma   weight residual
    1.524  1.313  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C7  PSC A 310 "
       pdb=" C8  PSC A 310 "
    ideal  model  delta    sigma   weight residual
    1.530  1.320  0.210 2.00e-02 2.50e+03 1.11e+02
  ... (remaining 7198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 9164
        3.02 -     6.03: 409
        6.03 -     9.05: 18
        9.05 -    12.07: 21
       12.07 -    15.08: 18
  Bond angle restraints: 9630
  Sorted by residual:
  angle pdb=" C10 PSC B 310 "
        pdb=" C9  PSC B 310 "
        pdb=" C8  PSC B 310 "
      ideal   model   delta    sigma   weight residual
     127.68  112.60   15.08 3.00e+00 1.11e-01 2.53e+01
  angle pdb=" C10 PSC A 310 "
        pdb=" C9  PSC A 310 "
        pdb=" C8  PSC A 310 "
      ideal   model   delta    sigma   weight residual
     127.68  112.60   15.08 3.00e+00 1.11e-01 2.53e+01
  angle pdb=" C10 PSC C 310 "
        pdb=" C9  PSC C 310 "
        pdb=" C8  PSC C 310 "
      ideal   model   delta    sigma   weight residual
     127.68  112.61   15.07 3.00e+00 1.11e-01 2.52e+01
  angle pdb=" C10 PSC B 310 "
        pdb=" C11 PSC B 310 "
        pdb=" C12 PSC B 310 "
      ideal   model   delta    sigma   weight residual
     111.07  126.14  -15.07 3.00e+00 1.11e-01 2.52e+01
  angle pdb=" C10 PSC A 310 "
        pdb=" C11 PSC A 310 "
        pdb=" C12 PSC A 310 "
      ideal   model   delta    sigma   weight residual
     111.07  126.12  -15.05 3.00e+00 1.11e-01 2.52e+01
  ... (remaining 9625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.98: 3690
       23.98 -    47.95: 294
       47.95 -    71.93: 90
       71.93 -    95.90: 0
       95.90 -   119.88: 3
  Dihedral angle restraints: 4077
    sinusoidal: 1824
      harmonic: 2253
  Sorted by residual:
  dihedral pdb=" C03 PSC C 302 "
           pdb=" O11 PSC C 302 "
           pdb=" P   PSC C 302 "
           pdb=" O12 PSC C 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.46   54.58  119.88     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C03 PSC A 302 "
           pdb=" O11 PSC A 302 "
           pdb=" P   PSC A 302 "
           pdb=" O12 PSC A 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.46   54.59  119.87     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C03 PSC B 302 "
           pdb=" O11 PSC B 302 "
           pdb=" P   PSC B 302 "
           pdb=" O12 PSC B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     174.46   54.60  119.86     1      3.00e+01 1.11e-03 1.60e+01
  ... (remaining 4074 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 457
       0.051 -    0.102: 326
       0.102 -    0.153: 113
       0.153 -    0.204: 31
       0.204 -    0.255: 9
  Chirality restraints: 936
  Sorted by residual:
  chirality pdb=" CA  PRO A 147 "
            pdb=" N   PRO A 147 "
            pdb=" C   PRO A 147 "
            pdb=" CB  PRO A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  PRO C 147 "
            pdb=" N   PRO C 147 "
            pdb=" C   PRO C 147 "
            pdb=" CB  PRO C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  PRO B 147 "
            pdb=" N   PRO B 147 "
            pdb=" C   PRO B 147 "
            pdb=" CB  PRO B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 933 not shown)

  Planarity restraints: 1158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 PSC B 312 "   -0.310 2.00e-02 2.50e+03   2.30e-01 5.28e+02
        pdb=" C11 PSC B 312 "    0.102 2.00e-02 2.50e+03
        pdb=" C8  PSC B 312 "   -0.100 2.00e-02 2.50e+03
        pdb=" C9  PSC B 312 "    0.308 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 PSC A 312 "   -0.310 2.00e-02 2.50e+03   2.30e-01 5.27e+02
        pdb=" C11 PSC A 312 "    0.102 2.00e-02 2.50e+03
        pdb=" C8  PSC A 312 "   -0.099 2.00e-02 2.50e+03
        pdb=" C9  PSC A 312 "    0.307 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 PSC C 312 "    0.310 2.00e-02 2.50e+03   2.30e-01 5.27e+02
        pdb=" C11 PSC C 312 "   -0.102 2.00e-02 2.50e+03
        pdb=" C8  PSC C 312 "    0.099 2.00e-02 2.50e+03
        pdb=" C9  PSC C 312 "   -0.307 2.00e-02 2.50e+03
  ... (remaining 1155 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1588
        2.79 -     3.32: 6677
        3.32 -     3.84: 12411
        3.84 -     4.37: 15914
        4.37 -     4.90: 25235
  Nonbonded interactions: 61825
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 103 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR C 103 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR B 103 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NH2 ARG C 171 "
            pdb=" O13 PSC C 309 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" NH2 ARG A 171 "
            pdb=" O13 PSC A 309 "
     model   vdw
     2.306 3.120
  ... (remaining 61820 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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=0.50 max=1.00 mean=0.99
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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.410
  Find NCS groups from input model:        0.060
  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:7.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
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   0.211   7206  Z= 0.877
  Angle     :  1.596  15.084   9630  Z= 0.937
  Chirality :  0.077   0.255    936
  Planarity :  0.023   0.230   1158
  Dihedral  : 17.842 119.879   2649
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  4.95 %
    Favored  : 94.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.27), residues: 780
  helix: -1.30 (0.19), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.76 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.003   ARG A 151 
 TYR   0.044   0.009   TYR A 150 
 PHE   0.035   0.008   PHE B 243 
 TRP   0.038   0.011   TRP B 187 
 HIS   0.011   0.006   HIS C 215 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01442 /  0.81 ( 7203)
  covalent geometry    : angle       1.59597 /  0.94 ( 9630)
  hydrogen bonds       : bond        0.19736 / 13.26 (  426)
  hydrogen bonds       : angle       7.30892 /  5.46 ( 1281)
  Misc. bond           : bond        0.16773 /  8.41 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm)
REVERT: A  230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp)
REVERT: B  207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm)
REVERT: C  207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm)
  outliers start: 6
  outliers final: 0
  residues processed: 79
  average time/residue: 0.5791
  time to fit residues: 48.2309
Evaluate side-chains
  63 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.0584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.103566 restraints weight = 27842.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.22
r_work: 0.3081 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7206  Z= 0.125
  Angle     :  0.551   5.944   9630  Z= 0.271
  Chirality :  0.040   0.124    936
  Planarity :  0.004   0.031   1158
  Dihedral  : 15.767  90.398   1268
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  6.31 %
    Favored  : 92.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.29), residues: 780
  helix:  1.62 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.20 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 151 
 TYR   0.010   0.001   TYR C 154 
 PHE   0.017   0.001   PHE B 134 
 TRP   0.022   0.002   TRP A  42 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.13 ( 7203)
  covalent geometry    : angle       0.55120 /  0.27 ( 9630)
  hydrogen bonds       : bond        0.04951 /  3.28 (  426)
  hydrogen bonds       : angle       3.99766 /  2.99 ( 1281)
  Misc. bond           : bond        0.00063 /  0.03 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8626 (t70) cc_final: 0.8280 (t70)
REVERT: A  171 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7332 (ttp-110)
REVERT: C  171 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7219 (ttp-110)
  outliers start: 4
  outliers final: 0
  residues processed: 82
  average time/residue: 0.5416
  time to fit residues: 46.8238
Evaluate side-chains
  58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 48 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0020
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 70 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.3394

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.098242 restraints weight = 39032.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.56
r_work: 0.3023 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7206  Z= 0.154
  Angle     :  0.583   5.872   9630  Z= 0.281
  Chirality :  0.042   0.131    936
  Planarity :  0.005   0.032   1158
  Dihedral  : 13.918  62.572   1266
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.81 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.29), residues: 780
  helix:  2.04 (0.20), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.30 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 176 
 TYR   0.011   0.002   TYR A 154 
 PHE   0.017   0.002   PHE A 134 
 TRP   0.019   0.002   TRP C  42 
 HIS   0.003   0.001   HIS B 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 7203)
  covalent geometry    : angle       0.58327 /  0.28 ( 9630)
  hydrogen bonds       : bond        0.05715 /  3.78 (  426)
  hydrogen bonds       : angle       3.93629 /  2.94 ( 1281)
  Misc. bond           : bond        0.00089 /  0.04 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8707 (t70) cc_final: 0.8377 (t70)
REVERT: A  171 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7358 (ttm110)
REVERT: B   51 MET cc_start: 0.8858 (mtm) cc_final: 0.8228 (mtm)
REVERT: B  174 LYS cc_start: 0.8090 (mttm) cc_final: 0.7779 (mtpp)
REVERT: C  121 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8008 (tp)
REVERT: C  244 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8340 (mtp180)
  outliers start: 4
  outliers final: 1
  residues processed: 74
  average time/residue: 0.5873
  time to fit residues: 45.5989
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain C residue  121 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 23 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    2.7188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.122333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.099654 restraints weight = 30831.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.28
r_work: 0.3037 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7206  Z= 0.164
  Angle     :  0.587   6.956   9630  Z= 0.280
  Chirality :  0.042   0.130    936
  Planarity :  0.005   0.032   1158
  Dihedral  : 13.523  57.594   1266
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.26 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.29), residues: 780
  helix:  2.11 (0.20), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.16 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 176 
 TYR   0.012   0.002   TYR C  81 
 PHE   0.017   0.002   PHE A 134 
 TRP   0.016   0.002   TRP A  42 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.16 ( 7203)
  covalent geometry    : angle       0.58682 /  0.28 ( 9630)
  hydrogen bonds       : bond        0.05834 /  3.86 (  426)
  hydrogen bonds       : angle       3.93078 /  2.94 ( 1281)
  Misc. bond           : bond        0.00085 /  0.04 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8700 (t70) cc_final: 0.8370 (t70)
REVERT: A  171 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7362 (ttm110)
REVERT: C  121 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8057 (tp)
REVERT: C  244 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8332 (mtp180)
  outliers start: 5
  outliers final: 1
  residues processed: 73
  average time/residue: 0.5849
  time to fit residues: 44.8678
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain C residue  121 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.3762

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.126234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.102894 restraints weight = 38642.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.55
r_work: 0.3068 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7206  Z= 0.118
  Angle     :  0.508   6.348   9630  Z= 0.242
  Chirality :  0.039   0.119    936
  Planarity :  0.004   0.031   1158
  Dihedral  : 12.281  59.606   1266
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  7.66 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.74 (0.29), residues: 780
  helix:  2.48 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.23 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 176 
 TYR   0.010   0.001   TYR B  81 
 PHE   0.016   0.001   PHE A 134 
 TRP   0.015   0.001   TRP A  42 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 7203)
  covalent geometry    : angle       0.50756 /  0.24 ( 9630)
  hydrogen bonds       : bond        0.04692 /  3.09 (  426)
  hydrogen bonds       : angle       3.72451 /  2.78 ( 1281)
  Misc. bond           : bond        0.00053 /  0.03 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8708 (t70) cc_final: 0.8379 (t70)
REVERT: A  121 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8093 (tp)
REVERT: A  171 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7313 (ttm110)
REVERT: C  244 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8274 (mtm-85)
  outliers start: 8
  outliers final: 1
  residues processed: 70
  average time/residue: 0.6157
  time to fit residues: 45.3240
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain C residue  137 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 50 optimal weight:   20.0000
   chunk 71 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    4.3990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.098529 restraints weight = 37360.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.40
r_work: 0.2995 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2993 r_free = 0.2993    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.2993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7206  Z= 0.227
  Angle     :  0.671   7.564   9630  Z= 0.317
  Chirality :  0.046   0.137    936
  Planarity :  0.005   0.035   1158
  Dihedral  : 13.546  58.945   1266
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.41 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 780
  helix:  1.95 (0.20), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.10 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 176 
 TYR   0.013   0.002   TYR C  81 
 PHE   0.017   0.002   PHE B 134 
 TRP   0.011   0.002   TRP A 190 
 HIS   0.003   0.001   HIS B 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00554 /  0.23 ( 7203)
  covalent geometry    : angle       0.67113 /  0.32 ( 9630)
  hydrogen bonds       : bond        0.06891 /  4.57 (  426)
  hydrogen bonds       : angle       4.07812 /  3.05 ( 1281)
  Misc. bond           : bond        0.00112 /  0.06 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8733 (t70) cc_final: 0.8447 (t70)
REVERT: A  171 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7349 (ttm110)
REVERT: B  174 LYS cc_start: 0.8306 (mttp) cc_final: 0.8021 (mttt)
  outliers start: 6
  outliers final: 3
  residues processed: 69
  average time/residue: 0.5202
  time to fit residues: 37.9902
Evaluate side-chains
  61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  207 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    3.1990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.122737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.100013 restraints weight = 34312.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.34
r_work: 0.3019 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7206  Z= 0.182
  Angle     :  0.604   7.490   9630  Z= 0.286
  Chirality :  0.043   0.128    936
  Planarity :  0.005   0.035   1158
  Dihedral  : 13.075  59.501   1266
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.71 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.29), residues: 780
  helix:  2.01 (0.20), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.09 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 176 
 TYR   0.012   0.002   TYR C  81 
 PHE   0.017   0.002   PHE A 134 
 TRP   0.012   0.002   TRP A  42 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.18 ( 7203)
  covalent geometry    : angle       0.60358 /  0.29 ( 9630)
  hydrogen bonds       : bond        0.06072 /  4.02 (  426)
  hydrogen bonds       : angle       3.96298 /  2.96 ( 1281)
  Misc. bond           : bond        0.00092 /  0.05 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8726 (t70) cc_final: 0.8414 (t70)
REVERT: A  171 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7363 (ttm110)
REVERT: C  244 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8336 (mtm-85)
  outliers start: 5
  outliers final: 3
  residues processed: 63
  average time/residue: 0.4986
  time to fit residues: 33.1428
Evaluate side-chains
  59 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  207 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    2.1990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.124674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.101884 restraints weight = 33916.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.35
r_work: 0.3049 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3055 r_free = 0.3055    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.3055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7206  Z= 0.145
  Angle     :  0.549   7.051   9630  Z= 0.261
  Chirality :  0.040   0.123    936
  Planarity :  0.005   0.035   1158
  Dihedral  : 12.344  59.715   1266
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  8.86 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.29), residues: 780
  helix:  2.25 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.18 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 176 
 TYR   0.011   0.001   TYR A  81 
 PHE   0.016   0.001   PHE B 134 
 TRP   0.014   0.002   TRP B 102 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 7203)
  covalent geometry    : angle       0.54868 /  0.26 ( 9630)
  hydrogen bonds       : bond        0.05356 /  3.53 (  426)
  hydrogen bonds       : angle       3.83478 /  2.86 ( 1281)
  Misc. bond           : bond        0.00068 /  0.03 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8699 (t70) cc_final: 0.8375 (t70)
REVERT: A  121 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8146 (tp)
REVERT: A  171 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7333 (ttm110)
REVERT: C  244 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.8330 (mtm-85)
  outliers start: 4
  outliers final: 3
  residues processed: 59
  average time/residue: 0.5666
  time to fit residues: 35.2412
Evaluate side-chains
  56 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  207 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.9584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.128662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.105133 restraints weight = 41810.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.61
r_work: 0.3082 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7206  Z= 0.107
  Angle     :  0.486   6.542   9630  Z= 0.232
  Chirality :  0.038   0.120    936
  Planarity :  0.005   0.034   1158
  Dihedral  : 11.298  58.967   1266
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.31 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.85 (0.30), residues: 780
  helix:  2.58 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.22 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 176 
 TYR   0.009   0.001   TYR B  81 
 PHE   0.014   0.001   PHE B 134 
 TRP   0.015   0.001   TRP B 102 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.11 ( 7203)
  covalent geometry    : angle       0.48616 /  0.23 ( 9630)
  hydrogen bonds       : bond        0.04317 /  2.83 (  426)
  hydrogen bonds       : angle       3.65404 /  2.72 ( 1281)
  Misc. bond           : bond        0.00038 /  0.02 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8657 (t70) cc_final: 0.8361 (t70)
REVERT: A  171 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7320 (ttm110)
REVERT: C  244 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8098 (mtm-85)
  outliers start: 3
  outliers final: 2
  residues processed: 61
  average time/residue: 0.5822
  time to fit residues: 37.4421
Evaluate side-chains
  54 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain C residue   33 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 65 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    0.0020
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    2.3594

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.124951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.101806 restraints weight = 38134.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.49
r_work: 0.3038 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7206  Z= 0.149
  Angle     :  0.558   6.834   9630  Z= 0.265
  Chirality :  0.041   0.128    936
  Planarity :  0.005   0.034   1158
  Dihedral  : 11.892  59.899   1266
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.76 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.29), residues: 780
  helix:  2.41 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.22 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 176 
 TYR   0.011   0.002   TYR B  81 
 PHE   0.016   0.001   PHE B 134 
 TRP   0.018   0.002   TRP B 102 
 HIS   0.003   0.001   HIS B 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 7203)
  covalent geometry    : angle       0.55761 /  0.26 ( 9630)
  hydrogen bonds       : bond        0.05393 /  3.56 (  426)
  hydrogen bonds       : angle       3.80559 /  2.84 ( 1281)
  Misc. bond           : bond        0.00066 /  0.03 (    3)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   87 ASP cc_start: 0.8703 (t70) cc_final: 0.8393 (t70)
REVERT: A  171 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7364 (ttm110)
REVERT: C  244 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8353 (mtm-85)
  outliers start: 3
  outliers final: 3
  residues processed: 58
  average time/residue: 0.5734
  time to fit residues: 34.9254
Evaluate side-chains
  58 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain C residue   33 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.123957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.101458 restraints weight = 31382.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.26
r_work: 0.3045 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3056
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3056 r_free = 0.3056    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3056
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7206  Z= 0.160
  Angle     :  0.582   7.531   9630  Z= 0.275
  Chirality :  0.041   0.128    936
  Planarity :  0.005   0.034   1158
  Dihedral  : 12.202  59.824   1266
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.76 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.29), residues: 780
  helix:  2.28 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.21 (0.42), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 176 
 TYR   0.011   0.002   TYR C  81 
 PHE   0.016   0.002   PHE B 134 
 TRP   0.020   0.002   TRP B 102 
 HIS   0.003   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 7203)
  covalent geometry    : angle       0.58206 /  0.28 ( 9630)
  hydrogen bonds       : bond        0.05688 /  3.76 (  426)
  hydrogen bonds       : angle       3.87783 /  2.89 ( 1281)
  Misc. bond           : bond        0.00073 /  0.04 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1861.16 seconds
wall clock time: 32 minutes 29.94 seconds (1949.94 seconds total)