Starting phenix.real_space_refine
on Tue Feb 11 16:51:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zap_39883/02_2025/8zap_39883.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zap_39883/02_2025/8zap_39883.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/8zap_39883/02_2025/8zap_39883.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zap_39883/02_2025/8zap_39883.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zap_39883/02_2025/8zap_39883.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zap_39883/02_2025/8zap_39883.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=   0.014
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      24      8.98       5
     S      57      5.16       5
     C    4323      2.51       5
     N     965      2.21       5
     O    1073      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6442
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2102
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 16, 'TRANS': 241}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2110
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 16, 'TRANS': 242}
    Chain: "C"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2110
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 16, 'TRANS': 242}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 28
          Unusual residues: {'  K': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          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: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 28
          Unusual residues: {'  K': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          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: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 28
          Unusual residues: {'  K': 8, 'RET': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          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: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 4.63, per 1000 atoms: 0.72
  Number of scatterers: 6442
  At special positions: 0
  Unit cell: (74.2, 73.85, 79.1, 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      24     19.00
     S      57     16.00
     O    1073      8.00
     N     965      7.00
     C    4323      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: 1.66
  Conformation dependent library (CDL) restraints added in 870.7 milliseconds
  

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      74.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 50
      removed outlier: 3.689A  pdb=" N   GLY A  50 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 67
    Processing helix  chain 'A' and resid 68 through 90
    Processing helix  chain 'A' and resid 105 through 122
      removed outlier: 3.585A  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 126
      No H-bonds generated for 'chain 'A' and resid 125 through 126'
    Processing helix  chain 'A' and resid 128 through 128
      No H-bonds generated for 'chain 'A' and resid 128 through 128'
    Processing helix  chain 'A' and resid 129 through 146
    Processing helix  chain 'A' and resid 149 through 178
      removed outlier: 3.722A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
      removed outlier: 3.585A  pdb=" N   LEU A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 199
    Processing helix  chain 'A' and resid 200 through 209
      removed outlier: 3.539A  pdb=" N   ILE A 204 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 3.585A  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: 3.688A  pdb=" N   GLY B  50 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 67
    Processing helix  chain 'B' and resid 68 through 90
    Processing helix  chain 'B' and resid 105 through 121
      removed outlier: 3.564A  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: 3.747A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
      removed outlier: 3.583A  pdb=" N   LEU B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 199
    Processing helix  chain 'B' and resid 200 through 209
      removed outlier: 3.572A  pdb=" N   ILE B 204 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE B 207 " --> pdb=" O   PRO B 203 " (cutoff:3.500A)
      removed outlier: 3.584A  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: 3.671A  pdb=" N   GLY C  50 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 68 through 90
    Processing helix  chain 'C' and resid 105 through 121
      removed outlier: 3.541A  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: 3.747A  pdb=" N   ALA C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 164  - end of helix
      removed outlier: 3.580A  pdb=" N   LEU C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 199
    Processing helix  chain 'C' and resid 200 through 209
      removed outlier: 3.546A  pdb=" N   ILE C 204 " --> pdb=" O   PRO C 200 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE C 207 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
      removed outlier: 3.585A  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

    417 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: 0.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1814
        1.34 -     1.46: 1947
        1.46 -     1.58: 2794
        1.58 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 6633
  Sorted by residual:
  bond pdb=" CA  PHE B 202 "
       pdb=" C   PHE B 202 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.011 1.23e-02 6.61e+03 7.98e-01
  bond pdb=" CA  PHE C 202 "
       pdb=" C   PHE C 202 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.011 1.23e-02 6.61e+03 7.90e-01
  bond pdb=" CA  PHE A 202 "
       pdb=" C   PHE A 202 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.010 1.23e-02 6.61e+03 7.21e-01
  bond pdb=" CA  GLY A 158 "
       pdb=" C   GLY A 158 "
    ideal  model  delta    sigma   weight residual
    1.516  1.507  0.009 1.12e-02 7.97e+03 6.88e-01
  bond pdb=" C   PHE B   3 "
       pdb=" N   TYR B   4 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.014 1.79e-02 3.12e+03 6.44e-01
  ... (remaining 6628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 8869
        1.89 -     3.78: 143
        3.78 -     5.67: 25
        5.67 -     7.56: 0
        7.56 -     9.46: 3
  Bond angle restraints: 9040
  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  129.95   -9.46 1.42e+00 4.96e-01 4.43e+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  129.57   -9.08 1.42e+00 4.96e-01 4.09e+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  129.53   -9.04 1.42e+00 4.96e-01 4.05e+01
  angle pdb=" N   VAL A 107 "
        pdb=" CA  VAL A 107 "
        pdb=" C   VAL A 107 "
      ideal   model   delta    sigma   weight residual
     113.00  109.03    3.97 1.30e+00 5.92e-01 9.34e+00
  angle pdb=" N   VAL C 107 "
        pdb=" CA  VAL C 107 "
        pdb=" C   VAL C 107 "
      ideal   model   delta    sigma   weight residual
     113.00  109.18    3.82 1.30e+00 5.92e-01 8.64e+00
  ... (remaining 9035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 3140
       15.94 -    31.87: 412
       31.87 -    47.80: 109
       47.80 -    63.73: 34
       63.73 -    79.67: 4
  Dihedral angle restraints: 3699
    sinusoidal: 1447
      harmonic: 2252
  Sorted by residual:
  dihedral pdb=" CA  ASP A   5 "
           pdb=" CB  ASP A   5 "
           pdb=" CG  ASP A   5 "
           pdb=" OD1 ASP A   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.00   55.00     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  ASP C   5 "
           pdb=" CB  ASP C   5 "
           pdb=" CG  ASP C   5 "
           pdb=" OD1 ASP C   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.10   54.10     1      2.00e+01 2.50e-03 9.93e+00
  dihedral pdb=" CA  THR C 109 "
           pdb=" C   THR C 109 "
           pdb=" N   THR C 110 "
           pdb=" CA  THR C 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.55  -15.45     0      5.00e+00 4.00e-02 9.55e+00
  ... (remaining 3696 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 488
       0.026 -    0.052: 274
       0.052 -    0.079: 116
       0.079 -    0.105: 32
       0.105 -    0.131: 18
  Chirality restraints: 928
  Sorted by residual:
  chirality pdb=" CA  THR C 110 "
            pdb=" N   THR C 110 "
            pdb=" C   THR C 110 "
            pdb=" CB  THR C 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  PHE C 144 "
            pdb=" N   PHE C 144 "
            pdb=" C   PHE C 144 "
            pdb=" CB  PHE C 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  PRO A 182 "
            pdb=" N   PRO A 182 "
            pdb=" C   PRO A 182 "
            pdb=" CB  PRO A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 925 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 132 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" C   ALA A 132 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ALA A 132 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 133 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  94 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO C  95 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  94 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO B  95 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B  95 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  95 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.22: 18
        2.22 -     2.95: 2986
        2.95 -     3.68: 12339
        3.68 -     4.41: 21831
        4.41 -     5.14: 34117
  Nonbonded interactions: 71291
  Sorted by model distance:
  nonbonded pdb=" K     K A 305 "
            pdb=" O   HOH A 405 "
     model   vdw
     1.487 2.850
  nonbonded pdb=" K     K B 305 "
            pdb=" O   HOH B 406 "
     model   vdw
     1.492 2.850
  nonbonded pdb=" K     K C 305 "
            pdb=" O   HOH C 406 "
     model   vdw
     1.495 2.850
  nonbonded pdb=" K     K B 305 "
            pdb=" O   HOH B 410 "
     model   vdw
     1.574 2.850
  nonbonded pdb=" K     K C 305 "
            pdb=" O   HOH C 410 "
     model   vdw
     1.584 2.850
  ... (remaining 71286 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 2 through 126 or resid 128 through 260 or resid 301 throug \ 
h 309))
  selection = (chain 'C' and (resid 2 through 126 or resid 128 through 260 or resid 301 throug \ 
h 309))
}

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:             50.550
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     13.240
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   76.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
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   0.032   6633  Z= 0.213
  Angle     :  0.597   9.456   9040  Z= 0.347
  Chirality :  0.040   0.131    928
  Planarity :  0.006   0.043   1111
  Dihedral  : 16.029  79.666   2267
  Min Nonbonded Distance : 1.487

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.52 %
    Favored  : 81.29 %
  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:  1.24 (0.30), residues: 768
  helix:  0.86 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop :  1.10 (0.43), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A 225 
 PHE   0.011   0.001   PHE C 134 
 TYR   0.012   0.001   TYR B  81 
 ARG   0.002   0.000   ARG A 151 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7669 (m-80)
REVERT: A  174 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7610 (mtpt)
REVERT: A  183 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6778 (mptt)
REVERT: A  227 PHE cc_start: 0.7707 (m-10) cc_final: 0.7436 (m-80)
REVERT: B    3 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7713 (m-80)
REVERT: B  174 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7695 (mtpt)
REVERT: B  183 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6830 (mptt)
REVERT: C    3 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7698 (m-80)
REVERT: C  174 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7663 (mtpt)
REVERT: C  227 PHE cc_start: 0.7695 (m-10) cc_final: 0.7477 (m-80)
  outliers start: 28
  outliers final: 12
  residues processed: 92
  average time/residue: 0.9933
  time to fit residues: 97.4415
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   24 LEU
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 LYS
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   24 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  174 LYS
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  174 LYS
Chi-restraints excluded: chain C residue  183 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.129723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116180 restraints weight = 5975.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 0.86
r_work: 0.3223 rms_B_bonded: 1.27 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 2.27 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6633  Z= 0.210
  Angle     :  0.519   5.209   9040  Z= 0.264
  Chirality :  0.039   0.144    928
  Planarity :  0.005   0.042   1111
  Dihedral  : 10.823  79.645    924
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 13.77 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.12 (0.29), residues: 768
  helix:  1.72 (0.20), residues: 525
  sheet:  None (None), residues: 0
  loop :  0.92 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  42 
 HIS   0.002   0.001   HIS A 215 
 PHE   0.015   0.001   PHE B 144 
 TYR   0.010   0.002   TYR B 180 
 ARG   0.001   0.000   ARG C 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7394 (m-80)
REVERT: A  183 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6690 (mptt)
REVERT: A  227 PHE cc_start: 0.7705 (m-10) cc_final: 0.7405 (m-80)
REVERT: B    3 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7513 (m-80)
REVERT: B   70 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8696 (m)
REVERT: B  183 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6677 (mptt)
REVERT: C    3 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7523 (m-80)
REVERT: C   70 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8682 (m)
REVERT: C  183 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6585 (mptt)
REVERT: C  227 PHE cc_start: 0.7666 (m-10) cc_final: 0.7373 (m-80)
  outliers start: 26
  outliers final: 8
  residues processed: 100
  average time/residue: 1.1395
  time to fit residues: 120.7224
Evaluate side-chains
  92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  183 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3326 r_free = 0.3326 target = 0.122595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108319 restraints weight = 6182.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 0.85
r_work: 0.3036 rms_B_bonded: 1.31 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 2.36 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.0957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6633  Z= 0.216
  Angle     :  0.511   5.248   9040  Z= 0.257
  Chirality :  0.039   0.154    928
  Planarity :  0.005   0.039   1111
  Dihedral  :  9.822  78.550    904
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.97 %
    Favored  : 80.84 %
  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:  2.33 (0.29), residues: 768
  helix:  1.92 (0.21), residues: 525
  sheet:  None (None), residues: 0
  loop :  0.91 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  42 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.017   0.001   PHE B 144 
 TYR   0.009   0.001   TYR A 180 
 ARG   0.001   0.000   ARG C 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7315 (m-80)
REVERT: A   70 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8704 (m)
REVERT: A  183 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6615 (mptt)
REVERT: A  227 PHE cc_start: 0.7642 (m-10) cc_final: 0.7344 (m-80)
REVERT: B    3 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7306 (m-80)
REVERT: B  183 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6573 (mptt)
REVERT: C    3 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7318 (m-80)
REVERT: C   70 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8695 (m)
REVERT: C  183 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6549 (mptt)
REVERT: C  227 PHE cc_start: 0.7649 (m-10) cc_final: 0.7380 (m-80)
  outliers start: 28
  outliers final: 10
  residues processed: 100
  average time/residue: 1.0747
  time to fit residues: 113.9570
Evaluate side-chains
  92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  183 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0040
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1998

-------------------------------------------------------------------------------
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 = 0.3468 r_free = 0.3468 target = 0.130147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.116659 restraints weight = 6008.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 0.87
r_work: 0.3174 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 2.18 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6633  Z= 0.263
  Angle     :  0.542   5.250   9040  Z= 0.273
  Chirality :  0.041   0.156    928
  Planarity :  0.005   0.040   1111
  Dihedral  :  9.623  83.307    904
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.52 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.27 (0.29), residues: 768
  helix:  1.89 (0.20), residues: 517
  sheet:  None (None), residues: 0
  loop :  0.86 (0.43), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  42 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.020   0.002   PHE B 144 
 TYR   0.011   0.002   TYR B 180 
 ARG   0.002   0.000   ARG B 176 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 71
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8717 (m)
REVERT: A  183 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6754 (mptt)
REVERT: B  183 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6682 (mptt)
REVERT: B  230 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7259 (tp)
REVERT: C   70 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8692 (m)
REVERT: C  183 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6662 (mptt)
REVERT: C  230 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7294 (tp)
  outliers start: 32
  outliers final: 18
  residues processed: 98
  average time/residue: 1.0930
  time to fit residues: 113.2766
Evaluate side-chains
  96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  230 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    0.0570
   chunk 24 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.8100

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.131726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.118199 restraints weight = 5667.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 0.87
r_work: 0.2967 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 2.32 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6633  Z= 0.206
  Angle     :  0.502   5.268   9040  Z= 0.252
  Chirality :  0.039   0.150    928
  Planarity :  0.005   0.039   1111
  Dihedral  :  9.297  79.631    904
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 14.82 %
    Favored  : 80.84 %
  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:  2.36 (0.29), residues: 768
  helix:  1.94 (0.20), residues: 524
  sheet:  None (None), residues: 0
  loop :  0.92 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  42 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.018   0.001   PHE B 144 
 TYR   0.008   0.001   TYR C  45 
 ARG   0.001   0.000   ARG A 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8693 (m)
REVERT: A  183 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6534 (mptt)
REVERT: A  227 PHE cc_start: 0.7563 (m-10) cc_final: 0.7229 (m-80)
REVERT: A  230 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7101 (tp)
REVERT: B  183 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6484 (mptt)
REVERT: B  230 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: C  183 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6465 (mptt)
REVERT: C  227 PHE cc_start: 0.7595 (m-10) cc_final: 0.7309 (m-80)
REVERT: C  230 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7284 (tp)
  outliers start: 29
  outliers final: 18
  residues processed: 96
  average time/residue: 1.0212
  time to fit residues: 104.0762
Evaluate side-chains
  97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 72
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain B residue  230 LEU
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  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  230 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.133086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119403 restraints weight = 5817.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 0.89
r_work: 0.3214 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 2.34 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6633  Z= 0.194
  Angle     :  0.492   5.248   9040  Z= 0.246
  Chirality :  0.038   0.143    928
  Planarity :  0.005   0.039   1111
  Dihedral  :  9.081  75.898    904
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.57 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.54 (0.30), residues: 768
  helix:  2.07 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.01 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  42 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.018   0.001   PHE B 144 
 TYR   0.008   0.001   TYR C 103 
 ARG   0.001   0.000   ARG B 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8718 (m)
REVERT: A  183 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6736 (mptt)
REVERT: A  227 PHE cc_start: 0.7686 (m-10) cc_final: 0.7403 (m-80)
REVERT: B  183 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6667 (mptt)
REVERT: B  230 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7201 (tp)
REVERT: C  183 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6666 (mptt)
REVERT: C  227 PHE cc_start: 0.7670 (m-10) cc_final: 0.7438 (m-80)
REVERT: C  230 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7338 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 100
  average time/residue: 1.0036
  time to fit residues: 106.7739
Evaluate side-chains
  100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain B residue  230 LEU
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  110 THR
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  230 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0040
   chunk 6 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4192

-------------------------------------------------------------------------------
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 = 0.3289 r_free = 0.3289 target = 0.121189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.106535 restraints weight = 6074.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 0.87
r_work: 0.3230 rms_B_bonded: 1.29 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 2.28 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6633  Z= 0.161
  Angle     :  0.466   5.293   9040  Z= 0.233
  Chirality :  0.037   0.138    928
  Planarity :  0.005   0.038   1111
  Dihedral  :  8.798  70.445    904
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.17 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.75 (0.30), residues: 768
  helix:  2.26 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.00 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  42 
 HIS   0.002   0.000   HIS A 225 
 PHE   0.012   0.001   PHE B 144 
 TYR   0.009   0.001   TYR C  45 
 ARG   0.001   0.000   ARG A 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (m)
REVERT: A  183 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6576 (mptt)
REVERT: A  227 PHE cc_start: 0.7601 (m-10) cc_final: 0.7331 (m-80)
REVERT: A  230 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7192 (tp)
REVERT: B  183 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6533 (mptt)
REVERT: C  183 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6470 (mptt)
REVERT: C  227 PHE cc_start: 0.7572 (m-10) cc_final: 0.7325 (m-80)
  outliers start: 22
  outliers final: 11
  residues processed: 100
  average time/residue: 0.9857
  time to fit residues: 104.9839
Evaluate side-chains
  98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain B residue  184 CYS
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  234 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.128357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.113826 restraints weight = 6014.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 0.94
r_work: 0.3222 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6633  Z= 0.191
  Angle     :  0.483   5.267   9040  Z= 0.242
  Chirality :  0.038   0.141    928
  Planarity :  0.005   0.038   1111
  Dihedral  :  8.299  72.090    892
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.02 %
    Favored  : 80.99 %
  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:  2.74 (0.30), residues: 768
  helix:  2.25 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.01 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  42 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.014   0.001   PHE B 144 
 TYR   0.008   0.001   TYR C 103 
 ARG   0.001   0.000   ARG A 171 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8699 (m)
REVERT: A  183 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6636 (mptt)
REVERT: A  227 PHE cc_start: 0.7633 (m-10) cc_final: 0.7365 (m-80)
REVERT: A  230 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7382 (tp)
REVERT: B  183 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6618 (mptt)
REVERT: C  183 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6517 (mptt)
REVERT: C  227 PHE cc_start: 0.7617 (m-10) cc_final: 0.7366 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 95
  average time/residue: 1.0169
  time to fit residues: 102.5781
Evaluate side-chains
  94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue   33 CYS
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  234 SER
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 54 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.133259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.119335 restraints weight = 5881.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 0.90
r_work: 0.3108 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 2.18 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6633  Z= 0.208
  Angle     :  0.498   5.234   9040  Z= 0.250
  Chirality :  0.039   0.145    928
  Planarity :  0.005   0.038   1111
  Dihedral  :  8.346  74.655    892
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.02 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.66 (0.30), residues: 768
  helix:  2.18 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.01 (0.45), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 225 
 PHE   0.017   0.001   PHE B 144 
 TYR   0.009   0.001   TYR C 103 
 ARG   0.001   0.000   ARG C 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (m)
REVERT: A  183 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6700 (mptt)
REVERT: A  227 PHE cc_start: 0.7636 (m-10) cc_final: 0.7385 (m-80)
REVERT: A  230 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7436 (tp)
REVERT: B  183 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6676 (mptt)
REVERT: C  183 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6524 (mptt)
REVERT: C  227 PHE cc_start: 0.7621 (m-10) cc_final: 0.7393 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 92
  average time/residue: 1.0831
  time to fit residues: 105.6104
Evaluate side-chains
  92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.123102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108153 restraints weight = 6140.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 0.93
r_work: 0.2963 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6633  Z= 0.207
  Angle     :  0.496   5.233   9040  Z= 0.249
  Chirality :  0.039   0.145    928
  Planarity :  0.005   0.038   1111
  Dihedral  :  8.310  74.632    892
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.17 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.65 (0.30), residues: 768
  helix:  2.16 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.01 (0.44), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  42 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.020   0.001   PHE B 144 
 TYR   0.009   0.001   TYR C 103 
 ARG   0.001   0.000   ARG C 186 

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

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

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1536 Ramachandran restraints generated.
    768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A   70 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8680 (m)
REVERT: A  183 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6557 (mptt)
REVERT: A  227 PHE cc_start: 0.7558 (m-10) cc_final: 0.7256 (m-80)
REVERT: A  230 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7376 (tp)
REVERT: B  183 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6542 (mptt)
REVERT: C  183 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6382 (mptt)
REVERT: C  227 PHE cc_start: 0.7571 (m-10) cc_final: 0.7285 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 92
  average time/residue: 1.0807
  time to fit residues: 105.3613
Evaluate side-chains
  92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   70 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue   70 SER
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  184 CYS
Chi-restraints excluded: chain C residue  234 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.134897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.120955 restraints weight = 5769.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 0.89
r_work: 0.3119 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6633  Z= 0.196
  Angle     :  0.490   5.215   9040  Z= 0.246
  Chirality :  0.039   0.142    928
  Planarity :  0.005   0.038   1111
  Dihedral  :  8.232  73.748    892
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.17 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.69 (0.30), residues: 768
  helix:  2.20 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop :  1.02 (0.45), residues: 244

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   0.018   0.001   PHE B 144 
 TYR   0.009   0.001   TYR C 103 
 ARG   0.001   0.000   ARG C 186 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5546.59 seconds
wall clock time: 102 minutes 7.85 seconds (6127.85 seconds total)