Starting phenix.real_space_refine
on Sat May 10 18:02:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ifu_35423/05_2025/8ifu_35423_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ifu_35423/05_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_35423/05_2025/8ifu_35423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ifu_35423/05_2025/8ifu_35423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ifu_35423/05_2025/8ifu_35423_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ifu_35423/05_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-5687/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: 6.87, per 1000 atoms: 1.02
  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: 2.04
  Conformation dependent library (CDL) restraints added in 900.5 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: 0.55
  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: 1.70

  Time building geometry restraints manager: 2.28 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:             11.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.610
  Find NCS groups from input model:        0.350
  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:14.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.610
-------------------------------------------------------------------------------
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      :  0.018   0.323   6906  Z= 1.286
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20747 (  405)
  hydrogen bonds       : angle       7.52770 ( 1206)
  covalent geometry    : bond        0.01664 ( 6900)
  covalent geometry    : angle       1.97196 ( 9330)
  Misc. bond           : bond        0.21223 (    6)

*********************** 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  : 0.752 
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: 0.9277
  time to fit residues: 191.5044
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  : 0.727 
-------------------------------------------------------------------------------
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   6906  Z= 0.159
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04885 (  405)
  hydrogen bonds       : angle       4.63579 ( 1206)
  covalent geometry    : bond        0.00359 ( 6900)
  covalent geometry    : angle       0.72029 ( 9330)
  Misc. bond           : bond        0.00337 (    6)

*********************** 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  : 0.800 
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: 0.6689 (OUTLIER) cc_final: 0.5883 (pp20)
REVERT: C    9 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5949 (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: 0.9427
  time to fit residues: 144.2999
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  : 0.676 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.126773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110499 restraints weight = 6209.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.23
r_work: 0.3128 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6906  Z= 0.132
  Angle     :  0.622   8.382   9330  Z= 0.289
  Chirality :  0.040   0.136    936
  Planarity :  0.006   0.043   1131
  Dihedral  : 22.567 133.025   1154
  Min Nonbonded Distance : 2.244

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:  1.93 (0.31), residues: 771
  helix:  1.97 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.14 (0.43), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  42 
 HIS   0.002   0.001   HIS C 250 
 PHE   0.015   0.001   PHE C 167 
 TYR   0.011   0.002   TYR C 180 
 ARG   0.003   0.000   ARG A  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  405)
  hydrogen bonds       : angle       4.25470 ( 1206)
  covalent geometry    : bond        0.00299 ( 6900)
  covalent geometry    : angle       0.62214 ( 9330)
  Misc. bond           : bond        0.00247 (    6)

*********************** 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
  141 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6272 (pp20)
REVERT: B    9 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6174 (pp20)
REVERT: C    9 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6111 (pp20)
REVERT: C   28 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7796 (ttp)
REVERT: C  171 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7322 (ttm110)
  outliers start: 37
  outliers final: 15
  residues processed: 134
  average time/residue: 1.0507
  time to fit residues: 149.6773
Evaluate side-chains
  113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0570
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.127259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.111549 restraints weight = 6243.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.18
r_work: 0.3146 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6906  Z= 0.120
  Angle     :  0.588   7.901   9330  Z= 0.273
  Chirality :  0.040   0.145    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 19.850 145.058   1151
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 13.09 %
    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:  2.37 (0.31), residues: 771
  helix:  2.17 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop :  0.17 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  42 
 HIS   0.002   0.001   HIS B 172 
 PHE   0.014   0.001   PHE B 167 
 TYR   0.010   0.001   TYR A 180 
 ARG   0.002   0.000   ARG B 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  405)
  hydrogen bonds       : angle       4.16709 ( 1206)
  covalent geometry    : bond        0.00271 ( 6900)
  covalent geometry    : angle       0.58817 ( 9330)
  Misc. bond           : bond        0.00221 (    6)

*********************** 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
  140 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A    9 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6306 (pp20)
REVERT: A   25 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7815 (mp)
REVERT: A  252 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7643 (mt-10)
REVERT: B    9 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6092 (pp20)
REVERT: B   68 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8391 (p)
REVERT: B  233 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7395 (mptt)
REVERT: C    9 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6057 (pp20)
REVERT: C   28 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7753 (ttp)
REVERT: C  171 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7185 (ttm110)
  outliers start: 37
  outliers final: 17
  residues processed: 133
  average time/residue: 1.0149
  time to fit residues: 143.2393
Evaluate side-chains
  121 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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   68 SER
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    3 PHE
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  233 LYS
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  183 LYS
Chi-restraints excluded: chain C residue  234 THR
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:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    3.1388

-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.117692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.102403 restraints weight = 6250.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.15
r_work: 0.3023 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.072   6906  Z= 0.323
  Angle     :  0.834   8.585   9330  Z= 0.396
  Chirality :  0.055   0.191    936
  Planarity :  0.006   0.036   1131
  Dihedral  : 21.209 148.218   1151
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 12.63 %
    Favored  : 81.43 %
  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:  1.82 (0.30), residues: 771
  helix:  1.88 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.15 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP C  42 
 HIS   0.005   0.002   HIS C 172 
 PHE   0.022   0.003   PHE A   3 
 TYR   0.023   0.003   TYR A 177 
 ARG   0.005   0.001   ARG A 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06312 (  405)
  hydrogen bonds       : angle       4.59431 ( 1206)
  covalent geometry    : bond        0.00785 ( 6900)
  covalent geometry    : angle       0.83440 ( 9330)
  Misc. bond           : bond        0.00429 (    6)

*********************** 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
  128 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 89
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6972 (t)
REVERT: A    9 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6235 (pp20)
REVERT: A  122 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7819 (mt-10)
REVERT: A  252 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7565 (mt-10)
REVERT: B    9 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6093 (pp20)
REVERT: B  252 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7562 (mt-10)
REVERT: C    4 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7090 (t)
REVERT: C    9 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5940 (pp20)
  outliers start: 39
  outliers final: 20
  residues processed: 120
  average time/residue: 1.0048
  time to fit residues: 128.2208
Evaluate side-chains
  109 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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   85 THR
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  122 GLU
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   56 LYS
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  122 GLU
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 B residue  252 GLU
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   85 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   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:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3393 r_free = 0.3393 target = 0.122447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107049 restraints weight = 6264.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.17
r_work: 0.3089 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6906  Z= 0.143
  Angle     :  0.625   8.345   9330  Z= 0.292
  Chirality :  0.042   0.149    936
  Planarity :  0.005   0.036   1131
  Dihedral  : 20.296 149.162   1151
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 14.00 %
    Favored  : 81.43 %
  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:  2.32 (0.30), residues: 771
  helix:  2.25 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.02 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  42 
 HIS   0.002   0.001   HIS C 172 
 PHE   0.014   0.001   PHE A 167 
 TYR   0.011   0.002   TYR A 177 
 ARG   0.002   0.000   ARG A  46 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04511 (  405)
  hydrogen bonds       : angle       4.30100 ( 1206)
  covalent geometry    : bond        0.00338 ( 6900)
  covalent geometry    : angle       0.62541 ( 9330)
  Misc. bond           : bond        0.00232 (    6)

*********************** 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
  122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7049 (t)
REVERT: A    9 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6236 (pp20)
REVERT: A  252 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7610 (mt-10)
REVERT: B    4 CYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6876 (t)
REVERT: B    9 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6087 (pp20)
REVERT: C    9 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5959 (pp20)
REVERT: C   28 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7677 (ttp)
REVERT: C  171 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7180 (ttm110)
  outliers start: 30
  outliers final: 15
  residues processed: 118
  average time/residue: 1.0221
  time to fit residues: 127.8807
Evaluate side-chains
  111 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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    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:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 26 optimal weight:    0.1980
   chunk 43 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.125697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.110340 restraints weight = 6244.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 1.17
r_work: 0.3136 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6906  Z= 0.114
  Angle     :  0.564   7.059   9330  Z= 0.264
  Chirality :  0.039   0.131    936
  Planarity :  0.005   0.035   1131
  Dihedral  : 19.169 150.629   1151
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 14.76 %
    Favored  : 80.97 %
  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 (0.31), residues: 771
  helix:  2.55 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.26 (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 225 
 PHE   0.013   0.001   PHE A 167 
 TYR   0.009   0.001   TYR C 180 
 ARG   0.001   0.000   ARG C 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  405)
  hydrogen bonds       : angle       4.13822 ( 1206)
  covalent geometry    : bond        0.00264 ( 6900)
  covalent geometry    : angle       0.56436 ( 9330)
  Misc. bond           : bond        0.00187 (    6)

*********************** 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: 28
    poor density    : 101
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7746 (mp)
REVERT: B    9 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6116 (pp20)
REVERT: C    4 CYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7106 (t)
REVERT: C    9 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6041 (pp20)
REVERT: C  171 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7185 (ttm110)
  outliers start: 28
  outliers final: 14
  residues processed: 128
  average time/residue: 0.9666
  time to fit residues: 131.5758
Evaluate side-chains
  113 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  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    4 CYS
Chi-restraints excluded: chain C residue    9 GLU
Chi-restraints excluded: chain C residue   24 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.122240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.106578 restraints weight = 6299.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 1.19
r_work: 0.3070 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6906  Z= 0.188
  Angle     :  0.670   7.391   9330  Z= 0.317
  Chirality :  0.045   0.185    936
  Planarity :  0.005   0.033   1131
  Dihedral  : 19.497 150.772   1148
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.53 %
    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:  2.36 (0.30), residues: 771
  helix:  2.22 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.21 (0.43), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  42 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.002   PHE A 242 
 TYR   0.014   0.002   TYR B 177 
 ARG   0.003   0.001   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05072 (  405)
  hydrogen bonds       : angle       4.38193 ( 1206)
  covalent geometry    : bond        0.00450 ( 6900)
  covalent geometry    : angle       0.66966 ( 9330)
  Misc. bond           : bond        0.00253 (    6)

*********************** 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
  119 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A    4 CYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7115 (t)
REVERT: B    4 CYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7053 (t)
REVERT: B    9 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6207 (pp20)
REVERT: C    4 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7169 (t)
REVERT: C    9 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6045 (pp20)
REVERT: C   28 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7890 (ttp)
REVERT: C  171 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7501 (ttm110)
  outliers start: 27
  outliers final: 19
  residues processed: 114
  average time/residue: 1.0793
  time to fit residues: 130.6658
Evaluate side-chains
  115 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  174 LYS
Chi-restraints excluded: chain A residue  234 THR
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  183 LYS
Chi-restraints excluded: chain C residue  234 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.124810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.109110 restraints weight = 6287.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.20
r_work: 0.3105 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6906  Z= 0.137
  Angle     :  0.597   6.865   9330  Z= 0.282
  Chirality :  0.041   0.153    936
  Planarity :  0.005   0.034   1131
  Dihedral  : 18.755 156.894   1148
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.44 %
    Favored  : 79.91 %
  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:  2.56 (0.31), residues: 771
  helix:  2.38 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.27 (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 A 172 
 PHE   0.013   0.001   PHE A 167 
 TYR   0.011   0.002   TYR B  22 
 ARG   0.002   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04330 (  405)
  hydrogen bonds       : angle       4.28127 ( 1206)
  covalent geometry    : bond        0.00320 ( 6900)
  covalent geometry    : angle       0.59704 ( 9330)
  Misc. bond           : bond        0.00201 (    6)

*********************** 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
  119 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.687 
Fit side-chains
REVERT: B    9 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6196 (pp20)
REVERT: C    9 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6116 (pp20)
REVERT: C   28 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7869 (ttp)
REVERT: C  171 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7470 (ttm110)
  outliers start: 24
  outliers final: 20
  residues processed: 114
  average time/residue: 0.9526
  time to fit residues: 115.7793
Evaluate side-chains
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
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  174 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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0040
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.9196

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.124643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.108952 restraints weight = 6300.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.20
r_work: 0.3101 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6906  Z= 0.141
  Angle     :  0.593   6.272   9330  Z= 0.283
  Chirality :  0.041   0.156    936
  Planarity :  0.005   0.034   1131
  Dihedral  : 17.859 158.469   1148
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.59 %
    Favored  : 80.06 %
  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:  2.58 (0.31), residues: 771
  helix:  2.39 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.28 (0.44), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  42 
 HIS   0.003   0.001   HIS C 225 
 PHE   0.012   0.001   PHE A 167 
 TYR   0.011   0.002   TYR B  22 
 ARG   0.002   0.000   ARG C   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04394 (  405)
  hydrogen bonds       : angle       4.27943 ( 1206)
  covalent geometry    : bond        0.00333 ( 6900)
  covalent geometry    : angle       0.59290 ( 9330)
  Misc. bond           : bond        0.00199 (    6)

********************** 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
  118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.726 
Fit side-chains
REVERT: B    9 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6238 (pp20)
REVERT: C    9 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6148 (pp20)
REVERT: C   28 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7891 (ttp)
REVERT: C  171 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7516 (ttm110)
  outliers start: 22
  outliers final: 19
  residues processed: 114
  average time/residue: 0.9957
  time to fit residues: 120.6326
Evaluate side-chains
  116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 PHE
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  174 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    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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0050
   chunk 5 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.6196

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.126982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.111309 restraints weight = 6291.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.21
r_work: 0.3134 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6906  Z= 0.118
  Angle     :  0.551   5.679   9330  Z= 0.262
  Chirality :  0.040   0.146    936
  Planarity :  0.005   0.035   1131
  Dihedral  : 17.262 160.307   1148
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.29 %
    Favored  : 80.06 %
  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:  2.81 (0.31), residues: 771
  helix:  2.55 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop :  0.40 (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 225 
 PHE   0.013   0.001   PHE A 167 
 TYR   0.010   0.002   TYR C 103 
 ARG   0.002   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  405)
  hydrogen bonds       : angle       4.19546 ( 1206)
  covalent geometry    : bond        0.00270 ( 6900)
  covalent geometry    : angle       0.55055 ( 9330)
  Misc. bond           : bond        0.00171 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5317.58 seconds
wall clock time: 92 minutes 33.28 seconds (5553.28 seconds total)