Starting phenix.real_space_refine
on Thu Sep 18 09:37:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cr3_30446/09_2025/7cr3_30446.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      88      5.16       5
     C   10240      2.51       5
     N    2716      2.21       5
     O    2880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15924
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2855
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 6, 'TRANS': 342}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 1126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1126
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 2, 'TRANS': 140}
  Restraints were copied for chains:
    B, D, G, C, E, H
  Time building chain proxies: 3.00, per 1000 atoms: 0.19
  Number of scatterers: 15924
  At special positions: 0
  Unit cell: (124.722, 124.722, 119.652, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      88     16.00
     O    2880      8.00
     N    2716      7.00
     C   10240      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=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 761.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3664

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 4 sheets defined
      80.9% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 86
    Processing helix  chain 'A' and resid 91 through 115
      removed outlier: 3.949A  pdb=" N   TYR A  95 " --> pdb=" O   TRP A  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 114 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE A 115 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 148
      removed outlier: 4.693A  pdb=" N   ILE A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 165
      removed outlier: 3.892A  pdb=" N   GLY A 159 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 184
    Processing helix  chain 'A' and resid 196 through 211
      removed outlier: 3.718A  pdb=" N   MET A 211 " --> pdb=" O   ARG A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 228
    Processing helix  chain 'A' and resid 228 through 254
    Processing helix  chain 'A' and resid 263 through 276
      removed outlier: 3.555A  pdb=" N   THR A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 305
      removed outlier: 4.784A  pdb=" N   LEU A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE A 300 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 329
      removed outlier: 3.914A  pdb=" N   GLY A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 350
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 3.546A  pdb=" N   THR A 366 " --> pdb=" O   TYR A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 559
    Processing helix  chain 'A' and resid 563 through 594
      removed outlier: 3.721A  pdb=" N   VAL A 567 " --> pdb=" O   ASP A 563 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 21
    Processing helix  chain 'F' and resid 30 through 40
    Processing helix  chain 'F' and resid 45 through 57
    Processing helix  chain 'F' and resid 66 through 75
      removed outlier: 3.640A  pdb=" N   ARG F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 76 through 80
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.690A  pdb=" N   PHE F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 111
    Processing helix  chain 'F' and resid 118 through 130
    Processing helix  chain 'F' and resid 138 through 146
      removed outlier: 3.672A  pdb=" N   PHE F 142 " --> pdb=" O   ASN F 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 86
    Processing helix  chain 'B' and resid 91 through 115
      removed outlier: 3.949A  pdb=" N   TYR B  95 " --> pdb=" O   TRP B  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR B 114 " --> pdb=" O   SER B 110 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE B 115 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 148
      removed outlier: 4.693A  pdb=" N   ILE B 128 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 165
      removed outlier: 3.892A  pdb=" N   GLY B 159 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 184
    Processing helix  chain 'B' and resid 196 through 211
      removed outlier: 3.718A  pdb=" N   MET B 211 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 228
    Processing helix  chain 'B' and resid 228 through 254
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 3.555A  pdb=" N   THR B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 305
      removed outlier: 4.784A  pdb=" N   LEU B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE B 300 " --> pdb=" O   THR B 296 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 329
      removed outlier: 3.914A  pdb=" N   GLY B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 350
    Processing helix  chain 'B' and resid 357 through 366
      removed outlier: 3.546A  pdb=" N   THR B 366 " --> pdb=" O   TYR B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 559
    Processing helix  chain 'B' and resid 563 through 594
      removed outlier: 3.721A  pdb=" N   VAL B 567 " --> pdb=" O   ASP B 563 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 21
    Processing helix  chain 'C' and resid 30 through 40
    Processing helix  chain 'C' and resid 45 through 57
    Processing helix  chain 'C' and resid 66 through 75
      removed outlier: 3.639A  pdb=" N   ARG C  75 " --> pdb=" O   THR C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 82 through 93
      removed outlier: 3.689A  pdb=" N   PHE C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 111
    Processing helix  chain 'C' and resid 118 through 130
    Processing helix  chain 'C' and resid 138 through 146
      removed outlier: 3.672A  pdb=" N   PHE C 142 " --> pdb=" O   ASN C 138 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 86
    Processing helix  chain 'D' and resid 91 through 115
      removed outlier: 3.949A  pdb=" N   TYR D  95 " --> pdb=" O   TRP D  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR D 114 " --> pdb=" O   SER D 110 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE D 115 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 148
      removed outlier: 4.693A  pdb=" N   ILE D 128 " --> pdb=" O   GLY D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 165
      removed outlier: 3.892A  pdb=" N   GLY D 159 " --> pdb=" O   ARG D 155 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 184
    Processing helix  chain 'D' and resid 196 through 211
      removed outlier: 3.718A  pdb=" N   MET D 211 " --> pdb=" O   ARG D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 215 through 228
    Processing helix  chain 'D' and resid 228 through 254
    Processing helix  chain 'D' and resid 263 through 276
      removed outlier: 3.555A  pdb=" N   THR D 276 " --> pdb=" O   LEU D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 305
      removed outlier: 4.784A  pdb=" N   LEU D 299 " --> pdb=" O   ALA D 295 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE D 300 " --> pdb=" O   THR D 296 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER D 303 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 306 through 329
      removed outlier: 3.914A  pdb=" N   GLY D 310 " --> pdb=" O   ALA D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 332 through 350
    Processing helix  chain 'D' and resid 357 through 366
      removed outlier: 3.546A  pdb=" N   THR D 366 " --> pdb=" O   TYR D 362 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 536 through 559
    Processing helix  chain 'D' and resid 563 through 594
      removed outlier: 3.721A  pdb=" N   VAL D 567 " --> pdb=" O   ASP D 563 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 21
    Processing helix  chain 'E' and resid 30 through 40
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 66 through 75
      removed outlier: 3.640A  pdb=" N   ARG E  75 " --> pdb=" O   THR E  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 80
    Processing helix  chain 'E' and resid 82 through 93
      removed outlier: 3.690A  pdb=" N   PHE E  93 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 111
    Processing helix  chain 'E' and resid 118 through 130
    Processing helix  chain 'E' and resid 138 through 146
      removed outlier: 3.672A  pdb=" N   PHE E 142 " --> pdb=" O   ASN E 138 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 71 through 86
    Processing helix  chain 'G' and resid 91 through 115
      removed outlier: 3.949A  pdb=" N   TYR G  95 " --> pdb=" O   TRP G  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR G 114 " --> pdb=" O   SER G 110 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE G 115 " --> pdb=" O   VAL G 111 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 118 through 148
      removed outlier: 4.693A  pdb=" N   ILE G 128 " --> pdb=" O   GLY G 124 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 155 through 165
      removed outlier: 3.892A  pdb=" N   GLY G 159 " --> pdb=" O   ARG G 155 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 166 through 184
    Processing helix  chain 'G' and resid 196 through 211
      removed outlier: 3.718A  pdb=" N   MET G 211 " --> pdb=" O   ARG G 207 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 215 through 228
    Processing helix  chain 'G' and resid 228 through 254
    Processing helix  chain 'G' and resid 263 through 276
      removed outlier: 3.555A  pdb=" N   THR G 276 " --> pdb=" O   LEU G 272 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 288 through 305
      removed outlier: 4.784A  pdb=" N   LEU G 299 " --> pdb=" O   ALA G 295 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE G 300 " --> pdb=" O   THR G 296 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER G 303 " --> pdb=" O   LEU G 299 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 306 through 329
      removed outlier: 3.914A  pdb=" N   GLY G 310 " --> pdb=" O   ALA G 306 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 332 through 350
    Processing helix  chain 'G' and resid 357 through 366
      removed outlier: 3.546A  pdb=" N   THR G 366 " --> pdb=" O   TYR G 362 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 536 through 559
    Processing helix  chain 'G' and resid 563 through 594
      removed outlier: 3.721A  pdb=" N   VAL G 567 " --> pdb=" O   ASP G 563 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 7 through 21
    Processing helix  chain 'H' and resid 30 through 40
    Processing helix  chain 'H' and resid 45 through 57
    Processing helix  chain 'H' and resid 66 through 75
      removed outlier: 3.640A  pdb=" N   ARG H  75 " --> pdb=" O   THR H  71 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 76 through 80
    Processing helix  chain 'H' and resid 82 through 93
      removed outlier: 3.690A  pdb=" N   PHE H  93 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 102 through 111
    Processing helix  chain 'H' and resid 118 through 130
    Processing helix  chain 'H' and resid 138 through 146
      removed outlier: 3.672A  pdb=" N   PHE H 142 " --> pdb=" O   ASN H 138 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 27 through 29
    Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 29
    Processing sheet with id=AA3, first strand: chain 'E' and resid 27 through 29
    Processing sheet with id=AA4, first strand: chain 'H' and resid 27 through 29

    1157 hydrogen bonds defined for protein.
    3447 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: 2.30

  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:
        1.23 -     1.34: 5144
        1.34 -     1.46: 3851
        1.46 -     1.58: 7113
        1.58 -     1.69: 0
        1.69 -     1.81: 148
  Bond restraints: 16256
  Sorted by residual:
  bond pdb=" CB  LYS C  31 "
       pdb=" CG  LYS C  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.30e-01
  bond pdb=" CB  LYS E  31 "
       pdb=" CG  LYS E  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 5.13e-01
  bond pdb=" CB  LYS F  31 "
       pdb=" CG  LYS F  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 5.13e-01
  bond pdb=" CB  LYS H  31 "
       pdb=" CG  LYS H  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 5.13e-01
  bond pdb=" C   LEU B 307 "
       pdb=" N   PRO B 308 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.28e-02 6.10e+03 5.10e-01
  ... (remaining 16251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 21425
        1.42 -     2.83: 407
        2.83 -     4.25: 59
        4.25 -     5.66: 29
        5.66 -     7.08: 4
  Bond angle restraints: 21924
  Sorted by residual:
  angle pdb=" N   GLY E 114 "
        pdb=" CA  GLY E 114 "
        pdb=" C   GLY E 114 "
      ideal   model   delta    sigma   weight residual
     110.77  115.23   -4.46 1.93e+00 2.68e-01 5.34e+00
  angle pdb=" N   GLY F 114 "
        pdb=" CA  GLY F 114 "
        pdb=" C   GLY F 114 "
      ideal   model   delta    sigma   weight residual
     110.77  115.23   -4.46 1.93e+00 2.68e-01 5.34e+00
  angle pdb=" N   GLY H 114 "
        pdb=" CA  GLY H 114 "
        pdb=" C   GLY H 114 "
      ideal   model   delta    sigma   weight residual
     110.77  115.23   -4.46 1.93e+00 2.68e-01 5.34e+00
  angle pdb=" N   GLY C 114 "
        pdb=" CA  GLY C 114 "
        pdb=" C   GLY C 114 "
      ideal   model   delta    sigma   weight residual
     110.77  115.20   -4.43 1.93e+00 2.68e-01 5.26e+00
  angle pdb=" NE  ARG A 581 "
        pdb=" CZ  ARG A 581 "
        pdb=" NH1 ARG A 581 "
      ideal   model   delta    sigma   weight residual
     121.50  119.23    2.27 1.00e+00 1.00e+00 5.14e+00
  ... (remaining 21919 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 8432
       17.07 -    34.14: 936
       34.14 -    51.21: 196
       51.21 -    68.28: 24
       68.28 -    85.35: 8
  Dihedral angle restraints: 9596
    sinusoidal: 3896
      harmonic: 5700
  Sorted by residual:
  dihedral pdb=" CA  PHE E  93 "
           pdb=" C   PHE E  93 "
           pdb=" N   ASP E  94 "
           pdb=" CA  ASP E  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  dihedral pdb=" CA  PHE H  93 "
           pdb=" C   PHE H  93 "
           pdb=" N   ASP H  94 "
           pdb=" CA  ASP H  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  dihedral pdb=" CA  PHE F  93 "
           pdb=" C   PHE F  93 "
           pdb=" N   ASP F  94 "
           pdb=" CA  ASP F  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  ... (remaining 9593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1348
       0.027 -    0.054: 736
       0.054 -    0.081: 256
       0.081 -    0.108: 48
       0.108 -    0.135: 16
  Chirality restraints: 2404
  Sorted by residual:
  chirality pdb=" CA  ILE C 101 "
            pdb=" N   ILE C 101 "
            pdb=" C   ILE C 101 "
            pdb=" CB  ILE C 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE H 101 "
            pdb=" N   ILE H 101 "
            pdb=" C   ILE H 101 "
            pdb=" CB  ILE H 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE E 101 "
            pdb=" N   ILE E 101 "
            pdb=" C   ILE E 101 "
            pdb=" CB  ILE E 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 2401 not shown)

  Planarity restraints: 2768
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE E  66 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO E  67 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO E  67 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E  67 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE F  66 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO F  67 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO F  67 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  67 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H  66 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO H  67 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO H  67 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO H  67 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2765 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 3163
        2.77 -     3.30: 16950
        3.30 -     3.83: 27407
        3.83 -     4.37: 32026
        4.37 -     4.90: 51243
  Nonbonded interactions: 130789
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  79 "
            pdb=" OH  TYR C 100 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" NE2 GLN B 341 "
            pdb=" O   LEU C 113 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" ND2 ASN A  79 "
            pdb=" OH  TYR F 100 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" ND2 ASN G  79 "
            pdb=" OH  TYR H 100 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" ND2 ASN D  79 "
            pdb=" OH  TYR E 100 "
     model   vdw
     2.238 3.120
  ... (remaining 130784 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'H'
}

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 group one per residue
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:             1.060
  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:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.660
  Find NCS groups from input model:        0.090
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
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      :  0.002   0.022  16256  Z= 0.120
  Angle     :  0.546   7.079  21924  Z= 0.336
  Chirality :  0.036   0.135   2404
  Planarity :  0.003   0.037   2768
  Dihedral  : 14.563  85.347   5932
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.24 (0.15), residues: 1936
  helix: -1.78 (0.10), residues: 1492
  sheet:  None (None), residues: 0
  loop : -2.80 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 581 
 TYR   0.009   0.001   TYR B  74 
 PHE   0.010   0.001   PHE A 240 
 TRP   0.008   0.001   TRP A 360 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (16256)
  covalent geometry    : angle       0.54598 (21924)
  hydrogen bonds       : bond        0.13043 ( 1157)
  hydrogen bonds       : angle       6.46847 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  415 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 415
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 TRP cc_start: 0.6879 (m100) cc_final: 0.6622 (t60)
REVERT: A  237 TYR cc_start: 0.8526 (t80) cc_final: 0.7756 (t80)
REVERT: A  555 PHE cc_start: 0.6555 (t80) cc_final: 0.6241 (t80)
REVERT: F   28 ILE cc_start: 0.5918 (mm) cc_final: 0.5590 (mm)
REVERT: B  157 TRP cc_start: 0.6872 (m100) cc_final: 0.6630 (t60)
REVERT: B  237 TYR cc_start: 0.8526 (t80) cc_final: 0.7771 (t80)
REVERT: B  555 PHE cc_start: 0.6563 (t80) cc_final: 0.6227 (t80)
REVERT: C   28 ILE cc_start: 0.5904 (mm) cc_final: 0.5549 (mm)
REVERT: C   86 ILE cc_start: 0.5150 (tt) cc_final: 0.4910 (tt)
REVERT: D  157 TRP cc_start: 0.6874 (m100) cc_final: 0.6621 (t60)
REVERT: D  237 TYR cc_start: 0.8536 (t80) cc_final: 0.7783 (t80)
REVERT: D  555 PHE cc_start: 0.6567 (t80) cc_final: 0.6222 (t80)
REVERT: E   28 ILE cc_start: 0.5954 (mm) cc_final: 0.5639 (mm)
REVERT: E   86 ILE cc_start: 0.5113 (tt) cc_final: 0.4836 (tt)
REVERT: G  157 TRP cc_start: 0.6864 (m100) cc_final: 0.6612 (t60)
REVERT: G  237 TYR cc_start: 0.8540 (t80) cc_final: 0.7773 (t80)
REVERT: G  555 PHE cc_start: 0.6556 (t80) cc_final: 0.6220 (t80)
REVERT: H   28 ILE cc_start: 0.5930 (mm) cc_final: 0.5609 (mm)
REVERT: H   86 ILE cc_start: 0.5099 (tt) cc_final: 0.4827 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 415
  average time/residue: 0.1702
  time to fit residues: 97.1047
Evaluate side-chains
  289 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0060
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.3602

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 HIS
A 350 ASN
A 575 HIS
F 144 GLN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 HIS
B 350 ASN
B 575 HIS
C 144 GLN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  96 HIS
D 350 ASN
D 357 HIS
D 575 HIS
E 144 GLN
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  96 HIS
G 350 ASN
G 357 HIS
G 575 HIS
H 144 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.206611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.165387 restraints weight = 30185.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.156860 restraints weight = 40869.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.154027 restraints weight = 28691.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.155008 restraints weight = 22851.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.155342 restraints weight = 16735.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  16256  Z= 0.230
  Angle     :  0.712   8.579  21924  Z= 0.366
  Chirality :  0.043   0.214   2404
  Planarity :  0.004   0.044   2768
  Dihedral  :  4.476  18.955   2180
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.02 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.17), residues: 1936
  helix: -0.47 (0.12), residues: 1532
  sheet:  None (None), residues: 0
  loop : -2.81 (0.26), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  87 
 TYR   0.018   0.002   TYR A  74 
 PHE   0.023   0.002   PHE H  90 
 TRP   0.008   0.001   TRP G 157 
 HIS   0.003   0.001   HIS B 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (16256)
  covalent geometry    : angle       0.71154 (21924)
  hydrogen bonds       : bond        0.04942 ( 1157)
  hydrogen bonds       : angle       5.08010 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 351
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6747 (tmtt) cc_final: 0.5936 (mtpp)
REVERT: A  142 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7194 (m-80)
REVERT: A  237 TYR cc_start: 0.8516 (t80) cc_final: 0.7659 (t80)
REVERT: A  546 MET cc_start: 0.5670 (tpp) cc_final: 0.5375 (tpp)
REVERT: B   76 LYS cc_start: 0.6724 (tmtt) cc_final: 0.5928 (mtpp)
REVERT: B  142 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7167 (m-80)
REVERT: B  237 TYR cc_start: 0.8524 (t80) cc_final: 0.7789 (t80)
REVERT: B  341 GLN cc_start: 0.5479 (mt0) cc_final: 0.5246 (mt0)
REVERT: B  546 MET cc_start: 0.5663 (tpp) cc_final: 0.5378 (tpp)
REVERT: C  112 ASN cc_start: 0.7820 (p0) cc_final: 0.7585 (p0)
REVERT: D  142 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7181 (m-80)
REVERT: D  237 TYR cc_start: 0.8529 (t80) cc_final: 0.7677 (t80)
REVERT: D  546 MET cc_start: 0.5655 (tpp) cc_final: 0.5378 (tpp)
REVERT: G   76 LYS cc_start: 0.6756 (tmtt) cc_final: 0.5960 (mtpp)
REVERT: G  142 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7199 (m-80)
REVERT: G  237 TYR cc_start: 0.8533 (t80) cc_final: 0.7676 (t80)
REVERT: G  341 GLN cc_start: 0.5447 (mt0) cc_final: 0.5198 (mt0)
REVERT: G  546 MET cc_start: 0.5648 (tpp) cc_final: 0.5376 (tpp)
  outliers start: 32
  outliers final: 25
  residues processed: 367
  average time/residue: 0.1589
  time to fit residues: 81.7997
Evaluate side-chains
  309 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 280
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  299 LEU
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 163 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 157 optimal weight:    3.9990
   chunk 154 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 142 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS
B 357 HIS
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.204608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.159205 restraints weight = 29667.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.140622 restraints weight = 36974.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.141098 restraints weight = 28548.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.141560 restraints weight = 15073.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.141301 restraints weight = 13528.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  16256  Z= 0.179
  Angle     :  0.692  11.959  21924  Z= 0.350
  Chirality :  0.041   0.150   2404
  Planarity :  0.003   0.026   2768
  Dihedral  :  4.334  18.426   2180
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.07 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.18), residues: 1936
  helix:  0.18 (0.12), residues: 1540
  sheet:  None (None), residues: 0
  loop : -2.57 (0.27), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  87 
 TYR   0.017   0.002   TYR B  74 
 PHE   0.019   0.002   PHE G 555 
 TRP   0.008   0.001   TRP B 344 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (16256)
  covalent geometry    : angle       0.69172 (21924)
  hydrogen bonds       : bond        0.04553 ( 1157)
  hydrogen bonds       : angle       4.68036 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 319
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6851 (tmtt) cc_final: 0.6005 (mtpp)
REVERT: A   83 ASN cc_start: 0.7547 (m110) cc_final: 0.7339 (m110)
REVERT: A  142 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7520 (m-80)
REVERT: A  237 TYR cc_start: 0.8514 (t80) cc_final: 0.7448 (t80)
REVERT: A  546 MET cc_start: 0.6162 (tpp) cc_final: 0.5626 (tpp)
REVERT: B   76 LYS cc_start: 0.6860 (tmtt) cc_final: 0.5956 (mtpp)
REVERT: B   83 ASN cc_start: 0.7551 (m110) cc_final: 0.7321 (m110)
REVERT: B  142 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7525 (m-80)
REVERT: B  237 TYR cc_start: 0.8593 (t80) cc_final: 0.7786 (t80)
REVERT: B  546 MET cc_start: 0.6109 (tpp) cc_final: 0.5592 (tpp)
REVERT: D   76 LYS cc_start: 0.6863 (tmtt) cc_final: 0.6015 (mtpp)
REVERT: D   83 ASN cc_start: 0.7592 (m110) cc_final: 0.7356 (m110)
REVERT: D  142 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7524 (m-80)
REVERT: D  237 TYR cc_start: 0.8500 (t80) cc_final: 0.7512 (t80)
REVERT: D  546 MET cc_start: 0.6110 (tpp) cc_final: 0.5584 (tpp)
REVERT: G   76 LYS cc_start: 0.6851 (tmtt) cc_final: 0.6014 (mtpp)
REVERT: G   83 ASN cc_start: 0.7564 (m110) cc_final: 0.7354 (m110)
REVERT: G  142 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7528 (m-80)
REVERT: G  237 TYR cc_start: 0.8517 (t80) cc_final: 0.7530 (t80)
REVERT: G  546 MET cc_start: 0.6151 (tpp) cc_final: 0.5631 (tpp)
  outliers start: 42
  outliers final: 25
  residues processed: 347
  average time/residue: 0.1542
  time to fit residues: 76.0395
Evaluate side-chains
  314 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 285
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  299 LEU
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 159 optimal weight:    3.9990
   chunk 156 optimal weight:    9.9990
   chunk 130 optimal weight:   40.0000
   chunk 18 optimal weight:    4.9990
   chunk 145 optimal weight:    0.0270
   chunk 75 optimal weight:    8.9990
   chunk 162 optimal weight:    4.9990
   chunk 83 optimal weight:   20.0000
   chunk 31 optimal weight:    0.9990
   overall best weight:    2.4046

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 361 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.204827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.158570 restraints weight = 29660.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.142657 restraints weight = 34284.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141289 restraints weight = 28291.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142247 restraints weight = 15942.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142211 restraints weight = 13849.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  16256  Z= 0.180
  Angle     :  0.678   9.236  21924  Z= 0.348
  Chirality :  0.041   0.129   2404
  Planarity :  0.003   0.029   2768
  Dihedral  :  4.273  20.666   2180
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.00 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.18), residues: 1936
  helix:  0.43 (0.12), residues: 1544
  sheet:  None (None), residues: 0
  loop : -2.37 (0.28), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  87 
 TYR   0.018   0.002   TYR B  74 
 PHE   0.029   0.002   PHE G 555 
 TRP   0.008   0.001   TRP G 360 
 HIS   0.002   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (16256)
  covalent geometry    : angle       0.67786 (21924)
  hydrogen bonds       : bond        0.04470 ( 1157)
  hydrogen bonds       : angle       4.50713 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 311
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6879 (tmtt) cc_final: 0.6008 (mtpp)
REVERT: A  142 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7494 (m-80)
REVERT: A  219 LYS cc_start: 0.7679 (mttt) cc_final: 0.7447 (tptt)
REVERT: A  237 TYR cc_start: 0.8496 (t80) cc_final: 0.7520 (t80)
REVERT: A  321 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7628 (tt0)
REVERT: A  546 MET cc_start: 0.5959 (tpp) cc_final: 0.5315 (tpp)
REVERT: F   86 ILE cc_start: 0.4477 (pt) cc_final: 0.4266 (pt)
REVERT: B   76 LYS cc_start: 0.6772 (tmtt) cc_final: 0.5890 (mtpp)
REVERT: B  142 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7486 (m-80)
REVERT: B  219 LYS cc_start: 0.7680 (mttt) cc_final: 0.7431 (tptt)
REVERT: B  237 TYR cc_start: 0.8562 (t80) cc_final: 0.7737 (t80)
REVERT: B  321 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (tt0)
REVERT: B  546 MET cc_start: 0.5960 (tpp) cc_final: 0.5327 (tpp)
REVERT: D   76 LYS cc_start: 0.6814 (tmtt) cc_final: 0.5951 (mtpp)
REVERT: D  142 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7501 (m-80)
REVERT: D  219 LYS cc_start: 0.7674 (mttt) cc_final: 0.7417 (tptt)
REVERT: D  237 TYR cc_start: 0.8491 (t80) cc_final: 0.7518 (t80)
REVERT: D  321 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7629 (tt0)
REVERT: D  544 CYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5348 (t)
REVERT: D  546 MET cc_start: 0.6013 (tpp) cc_final: 0.5299 (tpp)
REVERT: E   83 GLU cc_start: 0.4070 (tp30) cc_final: 0.2856 (tp30)
REVERT: G   76 LYS cc_start: 0.6814 (tmtt) cc_final: 0.5952 (mtpp)
REVERT: G  142 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7506 (m-80)
REVERT: G  219 LYS cc_start: 0.7658 (mttt) cc_final: 0.7432 (tptt)
REVERT: G  237 TYR cc_start: 0.8491 (t80) cc_final: 0.7513 (t80)
REVERT: G  321 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7622 (tt0)
REVERT: G  544 CYS cc_start: 0.6417 (OUTLIER) cc_final: 0.5508 (t)
REVERT: G  546 MET cc_start: 0.6015 (tpp) cc_final: 0.5288 (tpp)
  outliers start: 71
  outliers final: 47
  residues processed: 359
  average time/residue: 0.1480
  time to fit residues: 76.0732
Evaluate side-chains
  330 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 273
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 GLN
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  129 LEU
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  321 GLN
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain D residue  544 CYS
Chi-restraints excluded: chain G residue   77 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  299 LEU
Chi-restraints excluded: chain G residue  320 VAL
Chi-restraints excluded: chain G residue  321 GLN
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain G residue  544 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 39 optimal weight:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 158 optimal weight:    0.9990
   chunk 163 optimal weight:    1.9990
   chunk 186 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   chunk 132 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  79 ASN
A 204 GLN
A 361 GLN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
B 361 GLN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
D 361 GLN
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  79 ASN
G 204 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.209587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.170564 restraints weight = 29740.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.162671 restraints weight = 39722.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.159082 restraints weight = 29390.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.158753 restraints weight = 25635.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.158729 restraints weight = 17807.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16256  Z= 0.146
  Angle     :  0.663  11.651  21924  Z= 0.340
  Chirality :  0.040   0.136   2404
  Planarity :  0.003   0.028   2768
  Dihedral  :  4.145  17.756   2180
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 22.32 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.18), residues: 1936
  helix:  0.69 (0.12), residues: 1556
  sheet:  None (None), residues: 0
  loop : -2.13 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 107 
 TYR   0.015   0.001   TYR E 100 
 PHE   0.018   0.001   PHE B 555 
 TRP   0.007   0.001   TRP B 288 
 HIS   0.002   0.001   HIS D  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (16256)
  covalent geometry    : angle       0.66317 (21924)
  hydrogen bonds       : bond        0.04091 ( 1157)
  hydrogen bonds       : angle       4.28169 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 331
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6598 (tmtt) cc_final: 0.5921 (mtpp)
REVERT: A  130 GLU cc_start: 0.7327 (pp20) cc_final: 0.7015 (pp20)
REVERT: A  142 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7096 (m-80)
REVERT: A  237 TYR cc_start: 0.8333 (t80) cc_final: 0.7537 (t80)
REVERT: A  249 LEU cc_start: 0.9175 (mt) cc_final: 0.8958 (mp)
REVERT: A  321 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7661 (tt0)
REVERT: A  546 MET cc_start: 0.5565 (tpp) cc_final: 0.5003 (tpp)
REVERT: F   96 ASP cc_start: 0.4784 (OUTLIER) cc_final: 0.4361 (p0)
REVERT: F  113 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4813 (tp)
REVERT: B   76 LYS cc_start: 0.6538 (tmtt) cc_final: 0.5846 (mtpp)
REVERT: B  142 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7138 (m-80)
REVERT: B  237 TYR cc_start: 0.8337 (t80) cc_final: 0.7549 (t80)
REVERT: B  249 LEU cc_start: 0.9215 (mt) cc_final: 0.9001 (mp)
REVERT: B  342 SER cc_start: 0.5172 (OUTLIER) cc_final: 0.3920 (p)
REVERT: B  546 MET cc_start: 0.5543 (tpp) cc_final: 0.5052 (tpp)
REVERT: C  116 LYS cc_start: 0.8799 (mptt) cc_final: 0.8321 (mtmm)
REVERT: D   76 LYS cc_start: 0.6523 (tmtt) cc_final: 0.5894 (mtpp)
REVERT: D  130 GLU cc_start: 0.7327 (pp20) cc_final: 0.7009 (pp20)
REVERT: D  142 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7127 (m-80)
REVERT: D  237 TYR cc_start: 0.8328 (t80) cc_final: 0.7606 (t80)
REVERT: D  249 LEU cc_start: 0.9206 (mt) cc_final: 0.8990 (mp)
REVERT: D  546 MET cc_start: 0.5549 (tpp) cc_final: 0.5014 (tpp)
REVERT: G   76 LYS cc_start: 0.6549 (tmtt) cc_final: 0.5871 (mtpp)
REVERT: G  130 GLU cc_start: 0.7322 (pp20) cc_final: 0.7016 (pp20)
REVERT: G  142 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7145 (m-80)
REVERT: G  237 TYR cc_start: 0.8343 (t80) cc_final: 0.7617 (t80)
REVERT: G  249 LEU cc_start: 0.9254 (mt) cc_final: 0.9025 (mp)
REVERT: G  546 MET cc_start: 0.5454 (tpp) cc_final: 0.4894 (tpp)
REVERT: H   96 ASP cc_start: 0.4748 (OUTLIER) cc_final: 0.4337 (p0)
  outliers start: 45
  outliers final: 22
  residues processed: 361
  average time/residue: 0.1472
  time to fit residues: 75.7176
Evaluate side-chains
  315 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 284
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain F residue   96 ASP
Chi-restraints excluded: chain F residue  108 HIS
Chi-restraints excluded: chain F residue  113 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  127 TYR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 TYR
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  127 TYR
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   35 THR
Chi-restraints excluded: chain H residue   96 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 117 optimal weight:    0.8980
   chunk 81 optimal weight:    0.4980
   chunk 168 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 156 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 GLN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 204 GLN
** G  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 204 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.209705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.171013 restraints weight = 29655.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.162759 restraints weight = 39498.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.161749 restraints weight = 29460.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.161442 restraints weight = 21064.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.160162 restraints weight = 18648.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16256  Z= 0.154
  Angle     :  0.708  10.647  21924  Z= 0.357
  Chirality :  0.040   0.148   2404
  Planarity :  0.003   0.033   2768
  Dihedral  :  4.120  19.601   2180
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 22.14 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.18), residues: 1936
  helix:  0.85 (0.12), residues: 1556
  sheet:  None (None), residues: 0
  loop : -1.91 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 588 
 TYR   0.013   0.001   TYR D 347 
 PHE   0.014   0.001   PHE G 240 
 TRP   0.006   0.001   TRP B 344 
 HIS   0.003   0.001   HIS G 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (16256)
  covalent geometry    : angle       0.70788 (21924)
  hydrogen bonds       : bond        0.04166 ( 1157)
  hydrogen bonds       : angle       4.33714 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 302
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6484 (tmtt) cc_final: 0.5837 (mtpp)
REVERT: A  142 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7121 (m-80)
REVERT: A  237 TYR cc_start: 0.8386 (t80) cc_final: 0.7639 (t80)
REVERT: A  321 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (tt0)
REVERT: A  342 SER cc_start: 0.5295 (OUTLIER) cc_final: 0.3849 (p)
REVERT: A  546 MET cc_start: 0.5527 (tpp) cc_final: 0.5036 (tpp)
REVERT: B   76 LYS cc_start: 0.6486 (tmtt) cc_final: 0.5870 (mtpp)
REVERT: B  142 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7118 (m-80)
REVERT: B  237 TYR cc_start: 0.8394 (t80) cc_final: 0.7566 (t80)
REVERT: C   96 ASP cc_start: 0.4657 (OUTLIER) cc_final: 0.4316 (p0)
REVERT: C  116 LYS cc_start: 0.8856 (mptt) cc_final: 0.7993 (tttm)
REVERT: D   76 LYS cc_start: 0.6485 (tmtt) cc_final: 0.5881 (mtpp)
REVERT: D  142 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7105 (m-80)
REVERT: D  237 TYR cc_start: 0.8370 (t80) cc_final: 0.7638 (t80)
REVERT: D  546 MET cc_start: 0.5499 (tpp) cc_final: 0.5012 (tpp)
REVERT: E   96 ASP cc_start: 0.4750 (OUTLIER) cc_final: 0.4419 (p0)
REVERT: G   76 LYS cc_start: 0.6545 (tmtt) cc_final: 0.5885 (mtpp)
REVERT: G  142 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7146 (m-80)
REVERT: G  237 TYR cc_start: 0.8392 (t80) cc_final: 0.7662 (t80)
  outliers start: 59
  outliers final: 41
  residues processed: 346
  average time/residue: 0.1397
  time to fit residues: 69.7777
Evaluate side-chains
  322 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 273
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain F residue   35 THR
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue  108 HIS
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  127 TYR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 TYR
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   96 ASP
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  127 TYR
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  320 VAL
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   45 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 188 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 124 optimal weight:    9.9990
   chunk 33 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 146 optimal weight:    0.6980
   chunk 185 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
D 204 GLN
G  83 ASN
G 204 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.210168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.160215 restraints weight = 29890.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.153801 restraints weight = 21829.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.153911 restraints weight = 17789.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.154568 restraints weight = 16211.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.154921 restraints weight = 14739.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16256  Z= 0.155
  Angle     :  0.723  11.892  21924  Z= 0.361
  Chirality :  0.041   0.153   2404
  Planarity :  0.004   0.116   2768
  Dihedral  :  4.102  18.745   2180
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.92 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.18), residues: 1936
  helix:  0.95 (0.12), residues: 1556
  sheet:  None (None), residues: 0
  loop : -1.85 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 107 
 TYR   0.014   0.001   TYR F 100 
 PHE   0.014   0.001   PHE B 240 
 TRP   0.015   0.001   TRP B 344 
 HIS   0.003   0.001   HIS G 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (16256)
  covalent geometry    : angle       0.72343 (21924)
  hydrogen bonds       : bond        0.04170 ( 1157)
  hydrogen bonds       : angle       4.29895 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 301
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6801 (tmtt) cc_final: 0.5946 (mtpp)
REVERT: A  142 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7234 (m-80)
REVERT: A  237 TYR cc_start: 0.8347 (t80) cc_final: 0.7581 (t80)
REVERT: A  321 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7587 (tt0)
REVERT: A  589 VAL cc_start: 0.7633 (m) cc_final: 0.7287 (p)
REVERT: F   96 ASP cc_start: 0.4891 (OUTLIER) cc_final: 0.4495 (p0)
REVERT: B   76 LYS cc_start: 0.6669 (tmtt) cc_final: 0.5903 (mtpp)
REVERT: B  142 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7193 (m-80)
REVERT: B  237 TYR cc_start: 0.8313 (t80) cc_final: 0.7581 (t80)
REVERT: C   73 MET cc_start: 0.0343 (mmt) cc_final: -0.0355 (mtt)
REVERT: C   96 ASP cc_start: 0.4887 (OUTLIER) cc_final: 0.4471 (p0)
REVERT: C  116 LYS cc_start: 0.8937 (mptt) cc_final: 0.7968 (tttm)
REVERT: D   76 LYS cc_start: 0.6712 (tmtt) cc_final: 0.5946 (mtpp)
REVERT: D  142 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7180 (m-80)
REVERT: D  237 TYR cc_start: 0.8346 (t80) cc_final: 0.7665 (t80)
REVERT: D  546 MET cc_start: 0.5808 (tpp) cc_final: 0.5267 (tpp)
REVERT: E   96 ASP cc_start: 0.5068 (OUTLIER) cc_final: 0.4610 (p0)
REVERT: G   76 LYS cc_start: 0.6814 (tmtt) cc_final: 0.6020 (mtpp)
REVERT: G  142 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7242 (m-80)
REVERT: G  237 TYR cc_start: 0.8337 (t80) cc_final: 0.7652 (t80)
REVERT: G  546 MET cc_start: 0.5722 (tpp) cc_final: 0.5196 (tpp)
REVERT: H   96 ASP cc_start: 0.4948 (OUTLIER) cc_final: 0.4536 (p0)
  outliers start: 57
  outliers final: 37
  residues processed: 342
  average time/residue: 0.1390
  time to fit residues: 69.1931
Evaluate side-chains
  323 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 277
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue   96 ASP
Chi-restraints excluded: chain F residue  108 HIS
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  127 TYR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 TYR
Chi-restraints excluded: chain D residue  128 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   96 ASP
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  127 TYR
Chi-restraints excluded: chain G residue  128 ILE
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  320 VAL
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   96 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 178 optimal weight:    3.9990
   chunk 137 optimal weight:    9.9990
   chunk 161 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 132 optimal weight:   20.0000
   chunk 84 optimal weight:    4.9990
   chunk 130 optimal weight:    9.9990
   chunk 126 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
A  83 ASN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  78 GLN
D  79 ASN
D 204 GLN
G  78 GLN
G 204 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.208800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.169438 restraints weight = 30015.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.161591 restraints weight = 41937.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.159376 restraints weight = 29321.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159083 restraints weight = 22217.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.158329 restraints weight = 17711.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  16256  Z= 0.181
  Angle     :  0.772  11.854  21924  Z= 0.384
  Chirality :  0.042   0.149   2404
  Planarity :  0.005   0.145   2768
  Dihedral  :  4.220  19.718   2180
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 22.86 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.18), residues: 1936
  helix:  0.84 (0.12), residues: 1560
  sheet:  None (None), residues: 0
  loop : -1.84 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 588 
 TYR   0.016   0.001   TYR H 100 
 PHE   0.025   0.002   PHE E  20 
 TRP   0.021   0.001   TRP A 344 
 HIS   0.003   0.001   HIS B 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (16256)
  covalent geometry    : angle       0.77193 (21924)
  hydrogen bonds       : bond        0.04272 ( 1157)
  hydrogen bonds       : angle       4.43702 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 294
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6729 (tmtt) cc_final: 0.5938 (mtpp)
REVERT: A  142 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7152 (m-80)
REVERT: A  237 TYR cc_start: 0.8405 (t80) cc_final: 0.7643 (t80)
REVERT: A  321 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7740 (tt0)
REVERT: A  546 MET cc_start: 0.5520 (tpp) cc_final: 0.5039 (tpp)
REVERT: F   73 MET cc_start: 0.0726 (mmt) cc_final: 0.0064 (mtt)
REVERT: F   96 ASP cc_start: 0.5093 (OUTLIER) cc_final: 0.4719 (p0)
REVERT: B   76 LYS cc_start: 0.6463 (tmtt) cc_final: 0.5887 (mtpp)
REVERT: B  142 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7137 (m-80)
REVERT: B  183 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5303 (mm)
REVERT: B  237 TYR cc_start: 0.8416 (t80) cc_final: 0.7616 (t80)
REVERT: C   73 MET cc_start: 0.1077 (mmt) cc_final: 0.0180 (mtt)
REVERT: C   96 ASP cc_start: 0.5100 (OUTLIER) cc_final: 0.4633 (p0)
REVERT: D   76 LYS cc_start: 0.6569 (tmtt) cc_final: 0.5866 (mtpp)
REVERT: D  142 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7133 (m-80)
REVERT: D  237 TYR cc_start: 0.8388 (t80) cc_final: 0.7644 (t80)
REVERT: D  546 MET cc_start: 0.5598 (tpp) cc_final: 0.5109 (tpp)
REVERT: E   73 MET cc_start: 0.0585 (mmt) cc_final: -0.0441 (mtt)
REVERT: E   96 ASP cc_start: 0.5123 (OUTLIER) cc_final: 0.4760 (p0)
REVERT: E  100 TYR cc_start: 0.6391 (m-80) cc_final: 0.6166 (m-80)
REVERT: G   76 LYS cc_start: 0.6751 (tmtt) cc_final: 0.5951 (mtpp)
REVERT: G  142 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7172 (m-80)
REVERT: G  237 TYR cc_start: 0.8401 (t80) cc_final: 0.7654 (t80)
REVERT: H   73 MET cc_start: 0.0640 (mmt) cc_final: -0.0087 (mtt)
REVERT: H   96 ASP cc_start: 0.5079 (OUTLIER) cc_final: 0.4753 (p0)
  outliers start: 60
  outliers final: 38
  residues processed: 331
  average time/residue: 0.1308
  time to fit residues: 64.3984
Evaluate side-chains
  320 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 272
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  320 VAL
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue   96 ASP
Chi-restraints excluded: chain F residue  108 HIS
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  127 TYR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 TYR
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  234 THR
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  320 VAL
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   96 ASP
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  127 TYR
Chi-restraints excluded: chain G residue  142 PHE
Chi-restraints excluded: chain G residue  234 THR
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  320 VAL
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   96 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 144 optimal weight:   10.0000
   chunk 109 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0370
   chunk 12 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 141 optimal weight:    8.9990
   chunk 164 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 184 optimal weight:    7.9990
   overall best weight:    1.6064

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
D  83 ASN
D 204 GLN
G 204 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.210622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.173283 restraints weight = 29770.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.160672 restraints weight = 34100.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.159212 restraints weight = 37154.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.160513 restraints weight = 22414.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.161038 restraints weight = 18660.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.5087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  16256  Z= 0.153
  Angle     :  0.752  11.915  21924  Z= 0.373
  Chirality :  0.041   0.149   2404
  Planarity :  0.004   0.134   2768
  Dihedral  :  4.084  16.737   2180
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 23.15 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.18), residues: 1936
  helix:  0.95 (0.12), residues: 1552
  sheet:  None (None), residues: 0
  loop : -1.81 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 588 
 TYR   0.016   0.001   TYR C 100 
 PHE   0.032   0.002   PHE F  20 
 TRP   0.016   0.001   TRP D 344 
 HIS   0.004   0.001   HIS H 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (16256)
  covalent geometry    : angle       0.75182 (21924)
  hydrogen bonds       : bond        0.04062 ( 1157)
  hydrogen bonds       : angle       4.27899 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 289
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6389 (tmtt) cc_final: 0.5960 (mtpp)
REVERT: A  237 TYR cc_start: 0.8418 (t80) cc_final: 0.7617 (t80)
REVERT: A  321 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7671 (tt0)
REVERT: A  546 MET cc_start: 0.5426 (tpp) cc_final: 0.4971 (tpp)
REVERT: F   73 MET cc_start: 0.0843 (mmt) cc_final: 0.0145 (mtt)
REVERT: F   96 ASP cc_start: 0.5114 (OUTLIER) cc_final: 0.4592 (p0)
REVERT: B   76 LYS cc_start: 0.6355 (tmtt) cc_final: 0.5871 (mtpp)
REVERT: B  142 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7185 (m-80)
REVERT: B  237 TYR cc_start: 0.8380 (t80) cc_final: 0.7631 (t80)
REVERT: C   73 MET cc_start: 0.1008 (mmt) cc_final: -0.0024 (mtt)
REVERT: C   96 ASP cc_start: 0.5132 (OUTLIER) cc_final: 0.4669 (p0)
REVERT: D   76 LYS cc_start: 0.6232 (tmtt) cc_final: 0.5852 (mtpp)
REVERT: D  237 TYR cc_start: 0.8425 (t80) cc_final: 0.7663 (t80)
REVERT: D  546 MET cc_start: 0.5510 (tpp) cc_final: 0.5027 (tpp)
REVERT: E   73 MET cc_start: 0.0664 (mmt) cc_final: 0.0283 (mtt)
REVERT: E   96 ASP cc_start: 0.5133 (OUTLIER) cc_final: 0.4668 (p0)
REVERT: G   76 LYS cc_start: 0.6425 (tmtt) cc_final: 0.5983 (mtpp)
REVERT: G  237 TYR cc_start: 0.8409 (t80) cc_final: 0.7589 (t80)
REVERT: G  546 MET cc_start: 0.5520 (tpp) cc_final: 0.5082 (tpp)
REVERT: H   73 MET cc_start: 0.0687 (mmt) cc_final: 0.0012 (mtt)
REVERT: H   96 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4623 (p0)
  outliers start: 53
  outliers final: 36
  residues processed: 327
  average time/residue: 0.1252
  time to fit residues: 60.8797
Evaluate side-chains
  314 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 272
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  127 TYR
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  321 GLN
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  588 ARG
Chi-restraints excluded: chain F residue   45 THR
Chi-restraints excluded: chain F residue   96 ASP
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  127 TYR
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  322 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  127 TYR
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  273 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   96 ASP
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain G residue  109 LEU
Chi-restraints excluded: chain G residue  127 TYR
Chi-restraints excluded: chain G residue  244 ILE
Chi-restraints excluded: chain G residue  273 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  322 GLU
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   96 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 155 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0030
   chunk 96 optimal weight:   10.0000
   chunk 138 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 94 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 170 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 123 optimal weight:   20.0000
   chunk 125 optimal weight:    0.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 204 GLN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
C 144 GLN
D 204 GLN
** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  83 ASN
G 204 GLN
** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.212811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.174472 restraints weight = 29669.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.159647 restraints weight = 35584.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.155711 restraints weight = 40408.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.156790 restraints weight = 22548.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.157147 restraints weight = 17970.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16256  Z= 0.135
  Angle     :  0.774  16.979  21924  Z= 0.379
  Chirality :  0.041   0.198   2404
  Planarity :  0.004   0.119   2768
  Dihedral  :  4.006  17.061   2180
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.94 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.19), residues: 1936
  helix:  1.12 (0.13), residues: 1544
  sheet:  None (None), residues: 0
  loop : -1.73 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 107 
 TYR   0.015   0.001   TYR D 347 
 PHE   0.029   0.001   PHE H  20 
 TRP   0.017   0.001   TRP B 344 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (16256)
  covalent geometry    : angle       0.77373 (21924)
  hydrogen bonds       : bond        0.03878 ( 1157)
  hydrogen bonds       : angle       4.15992 ( 3447)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 289
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.6486 (tmtt) cc_final: 0.6004 (mtpp)
REVERT: A  237 TYR cc_start: 0.8288 (t80) cc_final: 0.7505 (t80)
REVERT: A  546 MET cc_start: 0.5690 (tpp) cc_final: 0.5207 (tpp)
REVERT: F   73 MET cc_start: 0.0419 (mmt) cc_final: -0.0246 (mtt)
REVERT: F   96 ASP cc_start: 0.5350 (OUTLIER) cc_final: 0.4852 (p0)
REVERT: B   76 LYS cc_start: 0.6306 (tmtt) cc_final: 0.5799 (mtpp)
REVERT: B  142 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7232 (m-80)
REVERT: B  237 TYR cc_start: 0.8350 (t80) cc_final: 0.7743 (t80)
REVERT: C   96 ASP cc_start: 0.5268 (OUTLIER) cc_final: 0.4738 (p0)
REVERT: C  110 MET cc_start: 0.5413 (tpt) cc_final: 0.5078 (tpt)
REVERT: D   76 LYS cc_start: 0.6293 (tmtt) cc_final: 0.5861 (mtpp)
REVERT: D  237 TYR cc_start: 0.8376 (t80) cc_final: 0.7818 (t80)
REVERT: D  546 MET cc_start: 0.5684 (tpp) cc_final: 0.5148 (tpp)
REVERT: E   73 MET cc_start: 0.0227 (mmt) cc_final: -0.0078 (mtt)
REVERT: E   96 ASP cc_start: 0.5379 (OUTLIER) cc_final: 0.4799 (p0)
REVERT: E  110 MET cc_start: 0.6635 (ppp) cc_final: 0.6286 (ppp)
REVERT: G   76 LYS cc_start: 0.6440 (tmtt) cc_final: 0.5974 (mtpp)
REVERT: G  237 TYR cc_start: 0.8323 (t80) cc_final: 0.7542 (t80)
REVERT: G  249 LEU cc_start: 0.9223 (mt) cc_final: 0.8984 (mp)
REVERT: G  546 MET cc_start: 0.5720 (tpp) cc_final: 0.5144 (tpp)
REVERT: H   73 MET cc_start: 0.0354 (mmt) cc_final: -0.0302 (mtt)
REVERT: H   96 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.4781 (p0)
  outliers start: 30
  outliers final: 19
  residues processed: 312
  average time/residue: 0.1370
  time to fit residues: 63.2697
Evaluate side-chains
  300 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 276
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  287 THR
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  588 ARG
Chi-restraints excluded: chain F residue   96 ASP
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  287 THR
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   45 THR
Chi-restraints excluded: chain C residue   96 ASP
Chi-restraints excluded: chain D residue  244 ILE
Chi-restraints excluded: chain D residue  287 THR
Chi-restraints excluded: chain D residue  324 HIS
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   96 ASP
Chi-restraints excluded: chain G residue  244 ILE
Chi-restraints excluded: chain G residue  287 THR
Chi-restraints excluded: chain G residue  324 HIS
Chi-restraints excluded: chain H residue   45 THR
Chi-restraints excluded: chain H residue   96 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 173 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 138 optimal weight:   10.0000
   chunk 135 optimal weight:    5.9990
   chunk 144 optimal weight:   10.0000
   chunk 145 optimal weight:    0.9990
   chunk 187 optimal weight:    0.3980
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 204 GLN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 GLN
D  78 GLN
D  83 ASN
D 204 GLN
** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  83 ASN
G 204 GLN
** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.212458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.166783 restraints weight = 29683.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.164615 restraints weight = 26695.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165725 restraints weight = 19034.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.165584 restraints weight = 15868.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165702 restraints weight = 13912.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.5602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16256  Z= 0.142
  Angle     :  0.820  16.375  21924  Z= 0.399
  Chirality :  0.042   0.187   2404
  Planarity :  0.004   0.108   2768
  Dihedral  :  4.012  20.016   2180
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 25.89 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.19), residues: 1936
  helix:  1.14 (0.13), residues: 1548
  sheet:  None (None), residues: 0
  loop : -1.49 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 588 
 TYR   0.016   0.001   TYR E 100 
 PHE   0.027   0.001   PHE H  20 
 TRP   0.039   0.001   TRP D 146 
 HIS   0.002   0.001   HIS G 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (16256)
  covalent geometry    : angle       0.81959 (21924)
  hydrogen bonds       : bond        0.03862 ( 1157)
  hydrogen bonds       : angle       4.16392 ( 3447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3015.12 seconds
wall clock time: 52 minutes 55.06 seconds (3175.06 seconds total)