Starting phenix.real_space_refine
on Tue Mar 11 16:27:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zao_39882/03_2025/8zao_39882_neut.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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
     K      15      8.98       5
     S      60      5.16       5
     C    4326      2.51       5
     N     966      2.21       5
     O    1065      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6432
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2109
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 16, 'TRANS': 242}
    Chain: "B"
      Number of atoms: 2109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2109
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 16, 'TRANS': 242}
    Chain: "C"
      Number of atoms: 2109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2109
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 16, 'TRANS': 242}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 25
          Unusual residues: {'  K': 5, 'RET': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 25
          Unusual residues: {'  K': 5, 'RET': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 25
          Unusual residues: {'  K': 5, 'RET': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 8.58, per 1000 atoms: 1.33
  Number of scatterers: 6432
  At special positions: 0
  Unit cell: (74.9, 73.5, 79.45, 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)
     K      15     19.00
     S      60     16.00
     O    1065      8.00
     N     966      7.00
     C    4326      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: 1.77
  Conformation dependent library (CDL) restraints added in 853.0 milliseconds
  

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      73.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 50
      removed outlier: 3.736A  pdb=" N   GLY A  50 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
    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: 3.740A  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 178
      removed outlier: 3.823A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
      removed outlier: 3.616A  pdb=" N   ARG A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 199
      removed outlier: 3.900A  pdb=" N   TRP A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TRP A 190 " --> pdb=" O   ARG A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 208
      removed outlier: 3.637A  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 50
      removed outlier: 3.743A  pdb=" N   GLY B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    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: 3.757A  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 178
      removed outlier: 3.822A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
      removed outlier: 3.588A  pdb=" N   ARG B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 199
      removed outlier: 3.907A  pdb=" N   TRP B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TRP B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 208
      removed outlier: 3.597A  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 50
      removed outlier: 3.743A  pdb=" N   GLY C  50 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
    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: 3.711A  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 178
      removed outlier: 3.821A  pdb=" N   ALA C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 164  - end of helix
      removed outlier: 3.619A  pdb=" N   ARG C 171 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 199
      removed outlier: 3.900A  pdb=" N   TRP C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TRP C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 208
      removed outlier: 3.632A  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

    414 hydrogen bonds defined for protein.
    1242 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: 1.79

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1814
        1.35 -     1.46: 1976
        1.46 -     1.58: 2768
        1.58 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 6639
  Sorted by residual:
  bond pdb=" C   TRP B 199 "
       pdb=" N   PRO B 200 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.19e-02 7.06e+03 2.64e+00
  bond pdb=" C   TRP A 199 "
       pdb=" N   PRO A 200 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.19e-02 7.06e+03 2.31e+00
  bond pdb=" C   TRP C 199 "
       pdb=" N   PRO C 200 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.018 1.19e-02 7.06e+03 2.24e+00
  bond pdb=" CA  PHE C 202 "
       pdb=" C   PHE C 202 "
    ideal  model  delta    sigma   weight residual
    1.520  1.532 -0.011 1.23e-02 6.61e+03 8.32e-01
  bond pdb=" C   PHE A 198 "
       pdb=" N   TRP A 199 "
    ideal  model  delta    sigma   weight residual
    1.332  1.344 -0.012 1.33e-02 5.65e+03 7.74e-01
  ... (remaining 6634 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 8835
        1.59 -     3.17: 184
        3.17 -     4.76: 14
        4.76 -     6.35: 12
        6.35 -     7.93: 3
  Bond angle restraints: 9048
  Sorted by residual:
  angle pdb=" C   GLY A  93 "
        pdb=" N   THR A  94 "
        pdb=" CA  THR A  94 "
      ideal   model   delta    sigma   weight residual
     120.49  128.42   -7.93 1.42e+00 4.96e-01 3.12e+01
  angle pdb=" C   GLY B  93 "
        pdb=" N   THR B  94 "
        pdb=" CA  THR B  94 "
      ideal   model   delta    sigma   weight residual
     120.49  128.40   -7.91 1.42e+00 4.96e-01 3.11e+01
  angle pdb=" C   GLY C  93 "
        pdb=" N   THR C  94 "
        pdb=" CA  THR C  94 "
      ideal   model   delta    sigma   weight residual
     120.49  128.40   -7.91 1.42e+00 4.96e-01 3.10e+01
  angle pdb=" C   TRP B 102 "
        pdb=" N   TYR B 103 "
        pdb=" CA  TYR B 103 "
      ideal   model   delta    sigma   weight residual
     121.54  126.21   -4.67 1.91e+00 2.74e-01 5.99e+00
  angle pdb=" C   TRP C 102 "
        pdb=" N   TYR C 103 "
        pdb=" CA  TYR C 103 "
      ideal   model   delta    sigma   weight residual
     121.54  126.16   -4.62 1.91e+00 2.74e-01 5.86e+00
  ... (remaining 9043 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3266
       17.99 -    35.99: 337
       35.99 -    53.98: 87
       53.98 -    71.97: 12
       71.97 -    89.97: 3
  Dihedral angle restraints: 3705
    sinusoidal: 1449
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" N   ARG A 244 "
           pdb=" CA  ARG A 244 "
           pdb=" CB  ARG A 244 "
           pdb=" CG  ARG A 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.20  -59.80     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ARG C 244 "
           pdb=" CA  ARG C 244 "
           pdb=" CB  ARG C 244 "
           pdb=" CG  ARG C 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.32  -59.68     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLU C 252 "
           pdb=" CB  GLU C 252 "
           pdb=" CG  GLU C 252 "
           pdb=" CD  GLU C 252 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.58   59.58     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 477
       0.024 -    0.047: 266
       0.047 -    0.071: 121
       0.071 -    0.095: 41
       0.095 -    0.119: 22
  Chirality restraints: 927
  Sorted by residual:
  chirality pdb=" CA  TYR A 103 "
            pdb=" N   TYR A 103 "
            pdb=" C   TYR A 103 "
            pdb=" CB  TYR A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.51e-01
  chirality pdb=" CA  TYR C 103 "
            pdb=" N   TYR C 103 "
            pdb=" C   TYR C 103 "
            pdb=" CB  TYR C 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.39e-01
  chirality pdb=" CA  TYR B 103 "
            pdb=" N   TYR B 103 "
            pdb=" C   TYR B 103 "
            pdb=" CB  TYR B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.35e-01
  ... (remaining 924 not shown)

  Planarity restraints: 1113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 199 "   -0.038 5.00e-02 4.00e+02   5.79e-02 5.36e+00
        pdb=" N   PRO C 200 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 200 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 200 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 199 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.33e+00
        pdb=" N   PRO B 200 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 200 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 200 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 199 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A 200 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 200 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 200 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1110 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.31: 22
        2.31 -     3.02: 3718
        3.02 -     3.72: 12654
        3.72 -     4.43: 21002
        4.43 -     5.14: 33112
  Nonbonded interactions: 70508
  Sorted by model distance:
  nonbonded pdb=" K     K C 302 "
            pdb=" O   HOH C 407 "
     model   vdw
     1.601 2.850
  nonbonded pdb=" K     K B 302 "
            pdb=" O   HOH B 407 "
     model   vdw
     1.602 2.850
  nonbonded pdb=" K     K A 302 "
            pdb=" O   HOH A 407 "
     model   vdw
     1.605 2.850
  nonbonded pdb=" K     K A 304 "
            pdb=" O   HOH A 404 "
     model   vdw
     1.995 2.850
  nonbonded pdb=" K     K B 302 "
            pdb=" O   HOH B 406 "
     model   vdw
     2.024 2.850
  ... (remaining 70503 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             10.430
  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:          0.350
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     22.920
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:14.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
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      :  0.003   0.033   6639  Z= 0.204
  Angle     :  0.571   7.935   9048  Z= 0.328
  Chirality :  0.038   0.119    927
  Planarity :  0.006   0.058   1113
  Dihedral  : 15.637  89.966   2271
  Min Nonbonded Distance : 1.601

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.25 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.30), residues: 771
  helix:  1.59 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.93 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  42 
 HIS   0.002   0.001   HIS C 225 
 PHE   0.011   0.001   PHE C 165 
 TYR   0.011   0.001   TYR B  81 
 ARG   0.001   0.000   ARG A  62 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7604 (mmmt)
REVERT: A  178 LEU cc_start: 0.8150 (mt) cc_final: 0.7799 (mm)
REVERT: B   14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7605 (mmmt)
REVERT: B  178 LEU cc_start: 0.8130 (mt) cc_final: 0.7774 (mm)
REVERT: B  230 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7587 (tp)
REVERT: C   14 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7624 (mmmt)
REVERT: C  178 LEU cc_start: 0.8170 (mt) cc_final: 0.7787 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 81
  average time/residue: 0.7589
  time to fit residues: 66.8237
Evaluate side-chains
  79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  233 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.3237 r_free = 0.3237 target = 0.106309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.093595 restraints weight = 7185.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.50
r_work: 0.3028 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.0726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6639  Z= 0.262
  Angle     :  0.530   5.518   9048  Z= 0.267
  Chirality :  0.039   0.128    927
  Planarity :  0.005   0.041   1113
  Dihedral  :  8.817  89.843    901
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.20 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.30), residues: 771
  helix:  1.75 (0.21), residues: 528
  sheet:  None (None), residues: 0
  loop :  1.02 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  42 
 HIS   0.002   0.001   HIS C 225 
 PHE   0.020   0.001   PHE A 144 
 TYR   0.010   0.002   TYR A  81 
 ARG   0.001   0.000   ARG A  62 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7594 (mmmt)
REVERT: A  201 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7355 (mtt)
REVERT: A  252 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7636 (mm-30)
REVERT: B   14 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7612 (mptt)
REVERT: B  183 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7091 (tppp)
REVERT: B  201 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7281 (mtt)
REVERT: B  230 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7380 (tp)
REVERT: B  252 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7747 (mm-30)
REVERT: C   14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7587 (mmmt)
REVERT: C  252 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7609 (mm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 100
  average time/residue: 0.8797
  time to fit residues: 94.2926
Evaluate side-chains
  91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  201 MET
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  201 MET
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3218 r_free = 0.3218 target = 0.104977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.092343 restraints weight = 7188.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.52
r_work: 0.2994 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.0955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6639  Z= 0.269
  Angle     :  0.522   5.496   9048  Z= 0.258
  Chirality :  0.039   0.124    927
  Planarity :  0.005   0.039   1113
  Dihedral  :  8.725  88.803    899
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 14.95 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.29), residues: 771
  helix:  1.67 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  0.87 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.024   0.001   PHE A 144 
 TYR   0.009   0.001   TYR C 180 
 ARG   0.001   0.000   ARG C  62 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7647 (mptt)
REVERT: A  183 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7138 (tppp)
REVERT: A  252 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7649 (mm-30)
REVERT: B   14 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7650 (mptt)
REVERT: B  183 LYS cc_start: 0.7404 (mtpp) cc_final: 0.7133 (tppp)
REVERT: B  230 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7445 (tp)
REVERT: B  252 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7794 (mm-30)
REVERT: C   14 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7626 (mmmt)
REVERT: C  183 LYS cc_start: 0.7449 (mtpp) cc_final: 0.7155 (tppp)
REVERT: C  252 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7662 (mm-30)
  outliers start: 24
  outliers final: 10
  residues processed: 92
  average time/residue: 0.9849
  time to fit residues: 96.6009
Evaluate side-chains
  88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3239 r_free = 0.3239 target = 0.107577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.094775 restraints weight = 7132.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.50
r_work: 0.3003 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6639  Z= 0.199
  Angle     :  0.489   5.512   9048  Z= 0.242
  Chirality :  0.037   0.116    927
  Planarity :  0.005   0.038   1113
  Dihedral  :  8.702  89.896    899
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.25 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.29), residues: 771
  helix:  1.77 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  0.89 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.022   0.001   PHE C 144 
 TYR   0.007   0.001   TYR B  81 
 ARG   0.001   0.000   ARG C 128 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7615 (mptt)
REVERT: A  183 LYS cc_start: 0.7334 (mtpp) cc_final: 0.7069 (tppp)
REVERT: A  252 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7628 (mm-30)
REVERT: B   14 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7615 (mptt)
REVERT: B  178 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7818 (mm)
REVERT: B  183 LYS cc_start: 0.7306 (mtpp) cc_final: 0.7060 (tppp)
REVERT: B  230 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7350 (tp)
REVERT: B  252 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7759 (mm-30)
REVERT: C   14 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7568 (mmmt)
REVERT: C  178 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: C  183 LYS cc_start: 0.7343 (mtpp) cc_final: 0.7075 (tppp)
REVERT: C  252 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7674 (mm-30)
  outliers start: 23
  outliers final: 10
  residues processed: 92
  average time/residue: 1.0121
  time to fit residues: 98.8938
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.105526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.092643 restraints weight = 7136.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 1.50
r_work: 0.2986 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   6639  Z= 0.303
  Angle     :  0.541   5.569   9048  Z= 0.264
  Chirality :  0.040   0.123    927
  Planarity :  0.005   0.039   1113
  Dihedral  :  8.664  87.950    899
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.50 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.29), residues: 771
  helix:  1.72 (0.21), residues: 534
  sheet:  None (None), residues: 0
  loop :  0.97 (0.44), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  42 
 HIS   0.003   0.001   HIS C 215 
 PHE   0.025   0.001   PHE B 144 
 TYR   0.010   0.002   TYR C 180 
 ARG   0.001   0.000   ARG A 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7570 (mmmt)
REVERT: A  183 LYS cc_start: 0.7399 (mtpp) cc_final: 0.7136 (tppp)
REVERT: A  252 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7680 (mm-30)
REVERT: B   14 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7647 (mptt)
REVERT: B  183 LYS cc_start: 0.7343 (mtpp) cc_final: 0.7081 (tppp)
REVERT: B  230 LEU cc_start: 0.7665 (tp) cc_final: 0.7449 (tp)
REVERT: B  252 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7771 (mm-30)
REVERT: C   14 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7594 (mmmt)
REVERT: C  183 LYS cc_start: 0.7403 (mtpp) cc_final: 0.7129 (tppp)
REVERT: C  252 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7687 (mm-30)
  outliers start: 25
  outliers final: 13
  residues processed: 91
  average time/residue: 1.1403
  time to fit residues: 110.8778
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 68 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3239 r_free = 0.3239 target = 0.107428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.094589 restraints weight = 7044.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.50
r_work: 0.3010 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6639  Z= 0.185
  Angle     :  0.486   5.492   9048  Z= 0.240
  Chirality :  0.037   0.117    927
  Planarity :  0.005   0.038   1113
  Dihedral  :  8.564  88.851    897
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.35 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.29), residues: 771
  helix:  1.84 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  0.89 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.017   0.001   PHE A 144 
 TYR   0.007   0.001   TYR C  45 
 ARG   0.001   0.000   ARG A 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7545 (mmmt)
REVERT: A  178 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: A  183 LYS cc_start: 0.7326 (mtpp) cc_final: 0.7080 (tppp)
REVERT: A  252 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7655 (mm-30)
REVERT: B   14 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7594 (mptt)
REVERT: B  178 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7821 (mm)
REVERT: B  183 LYS cc_start: 0.7289 (mtpp) cc_final: 0.7054 (tppp)
REVERT: B  252 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7722 (mt-10)
REVERT: C   14 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7588 (mmmt)
REVERT: C  178 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: C  183 LYS cc_start: 0.7346 (mtpp) cc_final: 0.7083 (tppp)
REVERT: C  252 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7674 (mm-30)
  outliers start: 28
  outliers final: 9
  residues processed: 97
  average time/residue: 1.0230
  time to fit residues: 105.9683
Evaluate side-chains
  83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.107308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.094398 restraints weight = 7019.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.50
r_work: 0.3007 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6639  Z= 0.210
  Angle     :  0.498   5.521   9048  Z= 0.246
  Chirality :  0.038   0.121    927
  Planarity :  0.005   0.041   1113
  Dihedral  :  8.519  87.302    897
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.84 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.29), residues: 771
  helix:  1.86 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  1.14 (0.45), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.020   0.001   PHE C 144 
 TYR   0.008   0.001   TYR C  81 
 ARG   0.001   0.000   ARG A 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7557 (mmmt)
REVERT: A  178 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7784 (mm)
REVERT: A  183 LYS cc_start: 0.7355 (mtpp) cc_final: 0.7123 (tppp)
REVERT: A  252 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7658 (mm-30)
REVERT: B   14 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7602 (mptt)
REVERT: B  178 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7838 (mm)
REVERT: B  183 LYS cc_start: 0.7298 (mtpp) cc_final: 0.7078 (tppp)
REVERT: B  252 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7745 (mm-30)
REVERT: C   14 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7596 (mmmt)
REVERT: C  178 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: C  183 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7108 (tppp)
REVERT: C  252 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7678 (mm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 90
  average time/residue: 1.0305
  time to fit residues: 98.8607
Evaluate side-chains
  86 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   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 = 0.3244 r_free = 0.3244 target = 0.108026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.095100 restraints weight = 7096.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.52
r_work: 0.3003 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6639  Z= 0.193
  Angle     :  0.495   5.500   9048  Z= 0.246
  Chirality :  0.038   0.125    927
  Planarity :  0.005   0.043   1113
  Dihedral  :  8.463  83.348    897
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 15.10 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.29), residues: 771
  helix:  1.92 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  1.14 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.024   0.001   PHE B 144 
 TYR   0.012   0.001   TYR A 103 
 ARG   0.001   0.000   ARG A 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7552 (mmmt)
REVERT: A  178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7769 (mm)
REVERT: A  183 LYS cc_start: 0.7320 (mtpp) cc_final: 0.7095 (tppp)
REVERT: A  252 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7596 (mt-10)
REVERT: B   14 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7580 (mptt)
REVERT: B  178 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7810 (mm)
REVERT: B  183 LYS cc_start: 0.7262 (mtpp) cc_final: 0.7050 (tppp)
REVERT: B  252 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7687 (mt-10)
REVERT: C   14 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7587 (mmmt)
REVERT: C  178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7762 (mm)
REVERT: C  183 LYS cc_start: 0.7326 (mtpp) cc_final: 0.7079 (tppp)
REVERT: C  252 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7682 (mm-30)
  outliers start: 27
  outliers final: 10
  residues processed: 97
  average time/residue: 0.9562
  time to fit residues: 98.9970
Evaluate side-chains
  85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.1980
   chunk 57 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
C  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.106550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.093600 restraints weight = 7193.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.50
r_work: 0.2998 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6639  Z= 0.199
  Angle     :  0.496   5.510   9048  Z= 0.247
  Chirality :  0.038   0.132    927
  Planarity :  0.005   0.041   1113
  Dihedral  :  8.470  81.568    897
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.70 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.29), residues: 771
  helix:  1.94 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  1.16 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.016   0.001   PHE B 144 
 TYR   0.007   0.001   TYR A 177 
 ARG   0.001   0.000   ARG C 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7546 (mmmt)
REVERT: A  178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: A  183 LYS cc_start: 0.7300 (mtpp) cc_final: 0.7084 (tppp)
REVERT: A  252 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: B   14 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7600 (mptt)
REVERT: B  178 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7819 (mm)
REVERT: B  183 LYS cc_start: 0.7273 (mtpp) cc_final: 0.7071 (tppp)
REVERT: B  252 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7713 (mm-30)
REVERT: C   14 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7585 (mmmt)
REVERT: C  178 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7764 (mm)
REVERT: C  183 LYS cc_start: 0.7333 (mtpp) cc_final: 0.7114 (tppp)
REVERT: C  252 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7689 (mm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 89
  average time/residue: 1.0250
  time to fit residues: 96.9833
Evaluate side-chains
  86 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  230 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    0.0670
   chunk 47 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.3240 r_free = 0.3240 target = 0.107232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.094260 restraints weight = 7144.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.52
r_work: 0.3031 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6639  Z= 0.188
  Angle     :  0.493   5.508   9048  Z= 0.246
  Chirality :  0.038   0.145    927
  Planarity :  0.005   0.041   1113
  Dihedral  :  8.459  80.323    897
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.59 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.29), residues: 771
  helix:  1.97 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  1.15 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 215 
 PHE   0.015   0.001   PHE B 144 
 TYR   0.007   0.001   TYR C  45 
 ARG   0.002   0.000   ARG B 151 

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7605 (mmmt)
REVERT: A  178 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7836 (mm)
REVERT: A  183 LYS cc_start: 0.7411 (mtpp) cc_final: 0.7202 (tppp)
REVERT: A  252 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7688 (mt-10)
REVERT: B   14 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7689 (mptt)
REVERT: B  178 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7877 (mm)
REVERT: B  252 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7712 (mm-30)
REVERT: C   14 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7635 (mmmt)
REVERT: C  178 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7828 (mm)
REVERT: C  183 LYS cc_start: 0.7423 (mtpp) cc_final: 0.7210 (tppp)
REVERT: C  252 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7740 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 87
  average time/residue: 1.0169
  time to fit residues: 94.0025
Evaluate side-chains
  84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  252 GLU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  178 LEU
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  252 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.106093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.093135 restraints weight = 7262.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.50
r_work: 0.3011 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6639  Z= 0.220
  Angle     :  0.508   5.550   9048  Z= 0.254
  Chirality :  0.039   0.162    927
  Planarity :  0.005   0.040   1113
  Dihedral  :  8.333  79.942    897
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.29 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.29), residues: 771
  helix:  1.93 (0.21), residues: 537
  sheet:  None (None), residues: 0
  loop :  1.14 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 138 
 HIS   0.003   0.001   HIS C 215 
 PHE   0.021   0.001   PHE A 144 
 TYR   0.008   0.001   TYR B 180 
 ARG   0.003   0.000   ARG B 151 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5540.96 seconds
wall clock time: 95 minutes 20.66 seconds (5720.66 seconds total)