Starting phenix.real_space_refine
on Tue Mar 11 21:07:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ifu_35423/03_2025/8ifu_35423_neut.cif"
  }
  resolution = 2.37
  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=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      42      5.16       5
     Na     48      4.78       5
     C    4548      2.51       5
     N     978      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 6732
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2095
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 14, 'TRANS': 244}
    Chain: "B"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2095
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 14, 'TRANS': 244}
    Chain: "C"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2095
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 14, 'TRANS': 244}
    Chain: "A"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 138
          Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          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: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 138
          Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          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: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 138
          Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          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: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "B"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "C"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 6.80, per 1000 atoms: 1.01
  Number of scatterers: 6732
  At special positions: 0
  Unit cell: (74.67, 74.67, 80.94, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       6     15.00
     Na     48     11.00
     O    1110      8.00
     N     978      7.00
     C    4548      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=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 931.5 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:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      72.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 50
      removed outlier: 4.076A  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 103 through 121
      removed outlier: 3.730A  pdb=" N   PHE A 108 " --> pdb=" O   LEU A 104 " (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 150 through 178
      Proline residue:  A 164  - end of helix
      removed outlier: 3.859A  pdb=" N   GLN A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 196
      removed outlier: 3.620A  pdb=" N   ILE A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP A 190 " --> pdb=" O   LYS A 186 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 194 " --> pdb=" O   TRP A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 207
      removed outlier: 3.921A  pdb=" N   ILE A 204 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU A 207 " --> pdb=" O   PRO A 203 " (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: 4.076A  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 103 through 121
      removed outlier: 3.730A  pdb=" N   PHE B 108 " --> pdb=" O   LEU B 104 " (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 150 through 178
      Proline residue:  B 164  - end of helix
      removed outlier: 3.858A  pdb=" N   GLN B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 196
      removed outlier: 3.620A  pdb=" N   ILE B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP B 190 " --> pdb=" O   LYS B 186 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B 194 " --> pdb=" O   TRP B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 207
      removed outlier: 3.921A  pdb=" N   ILE B 204 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 207 " --> pdb=" O   PRO B 203 " (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: 4.077A  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 103 through 121
      removed outlier: 3.730A  pdb=" N   PHE C 108 " --> pdb=" O   LEU C 104 " (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 150 through 178
      Proline residue:  C 164  - end of helix
      removed outlier: 3.859A  pdb=" N   GLN C 178 " --> pdb=" O   LYS C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 196
      removed outlier: 3.619A  pdb=" N   ILE C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP C 190 " --> pdb=" O   LYS C 186 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE C 194 " --> pdb=" O   TRP C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 207
      removed outlier: 3.921A  pdb=" N   ILE C 204 " --> pdb=" O   PRO C 200 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU C 207 " --> pdb=" O   PRO C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 233
    Processing helix  chain 'C' and resid 233 through 252

    405 hydrogen bonds defined for protein.
    1206 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: 1.87

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1026
        1.32 -     1.44: 2241
        1.44 -     1.56: 3561
        1.56 -     1.69: 18
        1.69 -     1.81: 54
  Bond restraints: 6900
  Sorted by residual:
  bond pdb=" C39 L9Q B 301 "
       pdb=" C40 L9Q B 301 "
    ideal  model  delta    sigma   weight residual
    1.333  1.523 -0.190 2.00e-02 2.50e+03 8.98e+01
  bond pdb=" C39 L9Q C 302 "
       pdb=" C40 L9Q C 302 "
    ideal  model  delta    sigma   weight residual
    1.333  1.522 -0.189 2.00e-02 2.50e+03 8.96e+01
  bond pdb=" C39 L9Q A 319 "
       pdb=" C40 L9Q A 319 "
    ideal  model  delta    sigma   weight residual
    1.333  1.522 -0.189 2.00e-02 2.50e+03 8.96e+01
  bond pdb=" C39 L9Q B 319 "
       pdb=" C40 L9Q B 319 "
    ideal  model  delta    sigma   weight residual
    1.333  1.522 -0.189 2.00e-02 2.50e+03 8.90e+01
  bond pdb=" C39 L9Q C 301 "
       pdb=" C40 L9Q C 301 "
    ideal  model  delta    sigma   weight residual
    1.333  1.522 -0.189 2.00e-02 2.50e+03 8.89e+01
  ... (remaining 6895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.76: 9171
        5.76 -    11.51: 126
       11.51 -    17.27: 21
       17.27 -    23.03: 6
       23.03 -    28.78: 6
  Bond angle restraints: 9330
  Sorted by residual:
  angle pdb=" C17 RET C 303 "
        pdb=" C1  RET C 303 "
        pdb=" C6  RET C 303 "
      ideal   model   delta    sigma   weight residual
     110.87   82.09   28.78 3.00e+00 1.11e-01 9.20e+01
  angle pdb=" C17 RET B 302 "
        pdb=" C1  RET B 302 "
        pdb=" C6  RET B 302 "
      ideal   model   delta    sigma   weight residual
     110.87   82.09   28.78 3.00e+00 1.11e-01 9.20e+01
  angle pdb=" C17 RET A 301 "
        pdb=" C1  RET A 301 "
        pdb=" C6  RET A 301 "
      ideal   model   delta    sigma   weight residual
     110.87   82.10   28.77 3.00e+00 1.11e-01 9.20e+01
  angle pdb=" C16 RET B 302 "
        pdb=" C1  RET B 302 "
        pdb=" C17 RET B 302 "
      ideal   model   delta    sigma   weight residual
     109.83   84.95   24.88 3.00e+00 1.11e-01 6.88e+01
  angle pdb=" C16 RET A 301 "
        pdb=" C1  RET A 301 "
        pdb=" C17 RET A 301 "
      ideal   model   delta    sigma   weight residual
     109.83   84.95   24.88 3.00e+00 1.11e-01 6.88e+01
  ... (remaining 9325 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.19: 3527
       35.19 -    70.38: 301
       70.38 -   105.57: 27
      105.57 -   140.75: 9
      140.75 -   175.94: 18
  Dihedral angle restraints: 3882
    sinusoidal: 1653
      harmonic: 2229
  Sorted by residual:
  dihedral pdb=" C   GLU B 248 "
           pdb=" N   GLU B 248 "
           pdb=" CA  GLU B 248 "
           pdb=" CB  GLU B 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.82   12.22     0      2.50e+00 1.60e-01 2.39e+01
  dihedral pdb=" C   GLU C 248 "
           pdb=" N   GLU C 248 "
           pdb=" CA  GLU C 248 "
           pdb=" CB  GLU C 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.80   12.20     0      2.50e+00 1.60e-01 2.38e+01
  dihedral pdb=" C   GLU A 248 "
           pdb=" N   GLU A 248 "
           pdb=" CA  GLU A 248 "
           pdb=" CB  GLU A 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.80   12.20     0      2.50e+00 1.60e-01 2.38e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 620
       0.116 -    0.232: 255
       0.232 -    0.348: 37
       0.348 -    0.463: 15
       0.463 -    0.579: 9
  Chirality restraints: 936
  Sorted by residual:
  chirality pdb=" CA  GLU A 248 "
            pdb=" N   GLU A 248 "
            pdb=" C   GLU A 248 "
            pdb=" CB  GLU A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.39e+00
  chirality pdb=" CA  GLU C 248 "
            pdb=" N   GLU C 248 "
            pdb=" C   GLU C 248 "
            pdb=" CB  GLU C 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.38e+00
  chirality pdb=" CA  GLU B 248 "
            pdb=" N   GLU B 248 "
            pdb=" C   GLU B 248 "
            pdb=" CB  GLU B 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.37e+00
  ... (remaining 933 not shown)

  Planarity restraints: 1131
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 L9Q C 301 "    0.336 2.00e-02 2.50e+03   3.25e-01 1.06e+03
        pdb=" C39 L9Q C 301 "   -0.364 2.00e-02 2.50e+03
        pdb=" C40 L9Q C 301 "   -0.284 2.00e-02 2.50e+03
        pdb=" C41 L9Q C 301 "    0.312 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 L9Q A 318 "    0.336 2.00e-02 2.50e+03   3.25e-01 1.06e+03
        pdb=" C39 L9Q A 318 "   -0.366 2.00e-02 2.50e+03
        pdb=" C40 L9Q A 318 "   -0.282 2.00e-02 2.50e+03
        pdb=" C41 L9Q A 318 "    0.312 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C38 L9Q B 319 "   -0.336 2.00e-02 2.50e+03   3.25e-01 1.06e+03
        pdb=" C39 L9Q B 319 "    0.365 2.00e-02 2.50e+03
        pdb=" C40 L9Q B 319 "    0.283 2.00e-02 2.50e+03
        pdb=" C41 L9Q B 319 "   -0.312 2.00e-02 2.50e+03
  ... (remaining 1128 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.11: 30
        2.11 -     2.81: 2166
        2.81 -     3.51: 8981
        3.51 -     4.20: 18754
        4.20 -     4.90: 31681
  Nonbonded interactions: 61612
  Sorted by model distance:
  nonbonded pdb=" C40 L9Q A 319 "
            pdb=" C40 L9Q B 301 "
     model   vdw
     1.417 2.912
  nonbonded pdb=" C40 L9Q B 301 "
            pdb=" C40 L9Q C 302 "
     model   vdw
     1.417 2.912
  nonbonded pdb=" C45 L9Q B 301 "
            pdb=" C27 L9Q B 319 "
     model   vdw
     1.489 3.840
  nonbonded pdb=" C27 L9Q A 318 "
            pdb=" C45 L9Q A 319 "
     model   vdw
     1.490 3.840
  nonbonded pdb=" C27 L9Q C 301 "
            pdb=" C45 L9Q C 302 "
     model   vdw
     1.490 3.840
  ... (remaining 61607 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 260 or resid 304 through 317))
  selection = (chain 'B' and (resid 2 through 260 or resid 304 through 317))
  selection = (chain 'C' and (resid 2 through 260 or resid 304 through 317))
}

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:             9.160
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.540
  Find NCS groups from input model:        0.330
  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:13.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
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      :  0.017   0.190   6900  Z= 1.069
  Angle     :  1.972  28.782   9330  Z= 1.024
  Chirality :  0.136   0.579    936
  Planarity :  0.021   0.325   1131
  Dihedral  : 27.728 175.942   2466
  Min Nonbonded Distance : 1.417

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  2.72 %
    Favored  : 96.89 %
  Rotamer:
    Outliers : 16.44 %
    Allowed  : 10.05 %
    Favored  : 73.52 %
  Cbeta Deviations :  1.69 %
  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: -2.87 (0.25), residues: 771
  helix: -1.99 (0.17), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.22 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP B 199 
 HIS   0.008   0.002   HIS A 250 
 PHE   0.034   0.003   PHE B 165 
 TYR   0.024   0.003   TYR A 177 
 ARG   0.003   0.001   ARG B 244 

*********************** 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
  230 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 108
    poor density    : 122
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  254 LEU cc_start: 0.8419 (mt) cc_final: 0.8194 (mp)
REVERT: B  254 LEU cc_start: 0.8361 (mt) cc_final: 0.8127 (mp)
REVERT: C   98 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7555 (m-80)
REVERT: C  254 LEU cc_start: 0.8404 (mt) cc_final: 0.8202 (mp)
  outliers start: 108
  outliers final: 17
  residues processed: 194
  average time/residue: 0.9305
  time to fit residues: 192.2193
Evaluate side-chains
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   68 SER
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue   98 PHE
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
B 125 HIS
B 219 GLN
C 125 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.128035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.111632 restraints weight = 6200.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.22
r_work: 0.3147 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6900  Z= 0.229
  Angle     :  0.720  10.218   9330  Z= 0.341
  Chirality :  0.043   0.153    936
  Planarity :  0.007   0.048   1131
  Dihedral  : 26.681 143.956   1157
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 14.00 %
    Favored  : 79.76 %
  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:  0.34 (0.29), residues: 771
  helix:  0.62 (0.20), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.51 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  42 
 HIS   0.003   0.001   HIS A 250 
 PHE   0.018   0.002   PHE C 167 
 TYR   0.014   0.002   TYR C 180 
 ARG   0.004   0.001   ARG A  46 

*********************** 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
  149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5980 (pp20)
REVERT: A  254 LEU cc_start: 0.8479 (mt) cc_final: 0.8263 (mp)
REVERT: B    9 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.5883 (pp20)
REVERT: C    9 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5950 (pp20)
REVERT: C  171 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7355 (ttm110)
REVERT: C  252 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7859 (mt-10)
  outliers start: 41
  outliers final: 16
  residues processed: 144
  average time/residue: 0.9496
  time to fit residues: 145.7068
Evaluate side-chains
  114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
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 0 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.126191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.109918 restraints weight = 6214.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.23
r_work: 0.3121 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6900  Z= 0.200
  Angle     :  0.626   8.619   9330  Z= 0.293
  Chirality :  0.041   0.136    936
  Planarity :  0.006   0.043   1131
  Dihedral  : 22.765 131.860   1154
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 13.70 %
    Favored  : 80.67 %
  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:  1.89 (0.30), residues: 771
  helix:  1.94 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.17 (0.43), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  42 
 HIS   0.003   0.001   HIS C 250 
 PHE   0.017   0.001   PHE C 167 
 TYR   0.012   0.002   TYR C 180 
 ARG   0.005   0.001   ARG A  46 

*********************** 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
  139 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6241 (pp20)
REVERT: B    9 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6160 (pp20)
REVERT: C    9 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6103 (pp20)
REVERT: C   28 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7807 (ttp)
REVERT: C  171 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7329 (ttm110)
REVERT: C  252 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7868 (mt-10)
  outliers start: 37
  outliers final: 15
  residues processed: 132
  average time/residue: 1.0528
  time to fit residues: 147.6575
Evaluate side-chains
  113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
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 30 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.122784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107153 restraints weight = 6248.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.17
r_work: 0.3089 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6900  Z= 0.237
  Angle     :  0.659   8.189   9330  Z= 0.308
  Chirality :  0.043   0.154    936
  Planarity :  0.005   0.037   1131
  Dihedral  : 20.656 141.395   1151
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 12.33 %
    Favored  : 81.74 %
  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:  2.07 (0.30), residues: 771
  helix:  2.08 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.12 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  42 
 HIS   0.003   0.001   HIS C 225 
 PHE   0.013   0.002   PHE B 167 
 TYR   0.014   0.002   TYR A 180 
 ARG   0.003   0.001   ARG B 244 

*********************** 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
  134 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 95
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6888 (t)
REVERT: A    9 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6272 (pp20)
REVERT: A  252 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7617 (mt-10)
REVERT: B    4 CYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6842 (t)
REVERT: B    9 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6070 (pp20)
REVERT: C    4 CYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6972 (t)
REVERT: C    9 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6024 (pp20)
REVERT: C   28 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7718 (ttp)
REVERT: C  171 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7191 (ttm110)
REVERT: C  252 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7788 (mt-10)
  outliers start: 39
  outliers final: 20
  residues processed: 128
  average time/residue: 1.0273
  time to fit residues: 139.6416
Evaluate side-chains
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    3 PHE
Chi-restraints excluded: chain B residue    4 CYS
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue   68 SER
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    4 CYS
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  183 LYS
Chi-restraints excluded: chain C residue  234 THR
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 67 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.119809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.104514 restraints weight = 6235.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.15
r_work: 0.3051 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6900  Z= 0.322
  Angle     :  0.716   8.275   9330  Z= 0.337
  Chirality :  0.046   0.168    936
  Planarity :  0.006   0.037   1131
  Dihedral  : 20.785 150.317   1151
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 12.33 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.99 (0.30), residues: 771
  helix:  2.01 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.09 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  42 
 HIS   0.004   0.001   HIS C 172 
 PHE   0.015   0.002   PHE A 242 
 TYR   0.016   0.002   TYR B 177 
 ARG   0.003   0.001   ARG C  46 

*********************** 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
  131 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.657 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6933 (t)
REVERT: A    9 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6225 (pp20)
REVERT: A  252 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7592 (mt-10)
REVERT: B    4 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6903 (t)
REVERT: B    9 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6057 (pp20)
REVERT: C    4 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6982 (t)
REVERT: C    9 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5963 (pp20)
REVERT: C   28 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7684 (ttp)
REVERT: C  171 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7282 (ttm110)
  outliers start: 36
  outliers final: 16
  residues processed: 123
  average time/residue: 1.0225
  time to fit residues: 133.5310
Evaluate side-chains
  113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    4 CYS
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    4 CYS
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  171 ARG
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.123819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108420 restraints weight = 6279.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.17
r_work: 0.3107 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6900  Z= 0.184
  Angle     :  0.595   7.774   9330  Z= 0.278
  Chirality :  0.040   0.140    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 19.870 150.340   1151
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 13.55 %
    Favored  : 81.74 %
  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:  2.44 (0.31), residues: 771
  helix:  2.36 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.03 (0.43), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 172 
 PHE   0.013   0.001   PHE A 167 
 TYR   0.010   0.001   TYR B 177 
 ARG   0.002   0.000   ARG C  46 

*********************** 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
  126 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6275 (pp20)
REVERT: A  252 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: B    9 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6103 (pp20)
REVERT: C    9 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5954 (pp20)
REVERT: C   28 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7704 (ttp)
REVERT: C  171 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7172 (ttm110)
  outliers start: 31
  outliers final: 15
  residues processed: 120
  average time/residue: 1.0190
  time to fit residues: 129.7503
Evaluate side-chains
  113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.124071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108708 restraints weight = 6261.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.17
r_work: 0.3111 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6900  Z= 0.184
  Angle     :  0.588   7.201   9330  Z= 0.275
  Chirality :  0.040   0.150    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 19.267 154.962   1151
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 13.85 %
    Favored  : 81.28 %
  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:  2.62 (0.31), residues: 771
  helix:  2.45 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.22 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  42 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 167 
 TYR   0.010   0.002   TYR B 177 
 ARG   0.001   0.000   ARG C 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
  129 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  183 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7907 (ttmt)
REVERT: A  252 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7576 (mt-10)
REVERT: B    4 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6984 (t)
REVERT: B    9 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6088 (pp20)
REVERT: B  238 LEU cc_start: 0.8307 (mt) cc_final: 0.8017 (mm)
REVERT: C    4 CYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6983 (t)
REVERT: C    9 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6043 (pp20)
REVERT: C   28 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7686 (ttp)
REVERT: C  171 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7167 (ttm110)
REVERT: C  252 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7489 (mt-10)
  outliers start: 32
  outliers final: 16
  residues processed: 126
  average time/residue: 0.9912
  time to fit residues: 132.8361
Evaluate side-chains
  120 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    4 CYS
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    4 CYS
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
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 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   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 = 0.3433 r_free = 0.3433 target = 0.126163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110509 restraints weight = 6276.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.20
r_work: 0.3122 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6900  Z= 0.188
  Angle     :  0.582   6.697   9330  Z= 0.274
  Chirality :  0.040   0.148    936
  Planarity :  0.005   0.035   1131
  Dihedral  : 18.630 158.024   1148
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.22 %
    Favored  : 80.82 %
  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 (0.31), residues: 771
  helix:  2.48 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.30 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.011   0.001   PHE A 167 
 TYR   0.009   0.002   TYR B  22 
 ARG   0.001   0.000   ARG A  46 

*********************** 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
  126 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7101 (t)
REVERT: A  183 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8091 (ttmt)
REVERT: A  252 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7675 (mt-10)
REVERT: B    4 CYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6982 (t)
REVERT: B    9 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6213 (pp20)
REVERT: C    4 CYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7175 (t)
REVERT: C    9 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6151 (pp20)
REVERT: C   28 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (ttp)
REVERT: C  171 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7490 (ttm110)
REVERT: C  252 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7587 (mt-10)
  outliers start: 26
  outliers final: 17
  residues processed: 122
  average time/residue: 0.9406
  time to fit residues: 122.4380
Evaluate side-chains
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain B residue    4 CYS
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    4 CYS
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
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 16 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0040
   chunk 73 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0040
   overall best weight:    0.4204

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

Flipped N/Q/H residues before XYZ refinement:
A 225 HIS
B 225 HIS
C 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.129202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.113619 restraints weight = 6276.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.21
r_work: 0.3164 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6900  Z= 0.147
  Angle     :  0.537   5.950   9330  Z= 0.253
  Chirality :  0.039   0.164    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 17.870 158.383   1148
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 15.68 %
    Favored  : 80.67 %
  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:  2.94 (0.31), residues: 771
  helix:  2.68 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.39 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  42 
 HIS   0.001   0.000   HIS A 225 
 PHE   0.011   0.001   PHE A 167 
 TYR   0.008   0.001   TYR C 180 
 ARG   0.004   0.000   ARG A 171 

*********************** 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
  132 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7997 (mp)
REVERT: A  183 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8025 (ttmt)
REVERT: B    9 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6260 (pp20)
REVERT: C    9 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6186 (pp20)
REVERT: C   28 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7963 (ttp)
REVERT: C  171 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7495 (ttm110)
  outliers start: 24
  outliers final: 15
  residues processed: 129
  average time/residue: 0.9613
  time to fit residues: 132.3268
Evaluate side-chains
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.124469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.108722 restraints weight = 6288.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.20
r_work: 0.3098 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6900  Z= 0.226
  Angle     :  0.604   6.186   9330  Z= 0.289
  Chirality :  0.043   0.179    936
  Planarity :  0.005   0.034   1131
  Dihedral  : 18.032 155.148   1148
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.29 %
    Favored  : 80.52 %
  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 (0.31), residues: 771
  helix:  2.42 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.36 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 172 
 PHE   0.011   0.001   PHE A 242 
 TYR   0.012   0.002   TYR B 177 
 ARG   0.003   0.001   ARG B 171 

********************** 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
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  183 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (ttmt)
REVERT: B    9 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6277 (pp20)
REVERT: C    9 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6168 (pp20)
REVERT: C   28 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7945 (ttp)
REVERT: C  171 ARG cc_start: 0.7856 (mtm110) cc_final: 0.7590 (ttm110)
  outliers start: 21
  outliers final: 16
  residues processed: 119
  average time/residue: 0.9035
  time to fit residues: 114.8811
Evaluate side-chains
  117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain B residue    9 GLU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  145 VAL
Chi-restraints excluded: chain B residue  170 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain C residue    3 PHE
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  133 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0030
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.4190

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.128857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113147 restraints weight = 6291.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.21
r_work: 0.3157 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6900  Z= 0.150
  Angle     :  0.530   5.462   9330  Z= 0.253
  Chirality :  0.039   0.168    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 17.370 156.240   1148
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.29 %
    Favored  : 80.37 %
  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:  2.98 (0.31), residues: 771
  helix:  2.68 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.50 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 172 
 PHE   0.012   0.001   PHE A 167 
 TYR   0.010   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 171 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5222.93 seconds
wall clock time: 89 minutes 44.00 seconds (5384.00 seconds total)