Starting phenix.real_space_refine
on Wed May 14 12:22:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fya_29562/05_2025/8fya_29562.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      57      5.49       5
     S      31      5.16       5
     C    7056      2.51       5
     N    2060      2.21       5
     O    2229      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11433
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2295
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "C"
      Number of atoms: 2388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2388
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 13, 'TRANS': 291}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 746
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1865
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 8, 'TRANS': 232}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2186
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
    Chain: "G"
      Number of atoms: 573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 573
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
    Chain: "H"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 30}
  Time building chain proxies: 7.61, per 1000 atoms: 0.67
  Number of scatterers: 11433
  At special positions: 0
  Unit cell: (93.66, 90.315, 142.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P      57     15.00
     O    2229      8.00
     N    2060      7.00
     C    7056      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: 3.09
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 8 sheets defined
      51.2% alpha, 15.4% beta
      20 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 4.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 19
    Processing helix  chain 'A' and resid 20 through 22
      No H-bonds generated for 'chain 'A' and resid 20 through 22'
    Processing helix  chain 'A' and resid 36 through 49
      removed outlier: 3.823A  pdb=" N   GLU A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 55
    Processing helix  chain 'B' and resid 67 through 77
    Processing helix  chain 'B' and resid 86 through 89
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 3.982A  pdb=" N   ASN B 114 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 129
    Processing helix  chain 'B' and resid 139 through 163
    Processing helix  chain 'B' and resid 180 through 205
    Processing helix  chain 'B' and resid 219 through 231
      removed outlier: 3.872A  pdb=" N   LEU B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   TYR B 229 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   ALA B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 244
    Processing helix  chain 'B' and resid 250 through 265
      removed outlier: 4.343A  pdb=" N   ASP B 265 " --> pdb=" O   ASP B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 280
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 304 through 306
      No H-bonds generated for 'chain 'B' and resid 304 through 306'
    Processing helix  chain 'C' and resid 17 through 21
      removed outlier: 3.871A  pdb=" N   ARG C  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 53
      No H-bonds generated for 'chain 'C' and resid 51 through 53'
    Processing helix  chain 'C' and resid 68 through 77
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.517A  pdb=" N   ASN C 114 " --> pdb=" O   GLU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 130
    Processing helix  chain 'C' and resid 139 through 163
    Processing helix  chain 'C' and resid 180 through 205
    Processing helix  chain 'C' and resid 219 through 231
      removed outlier: 3.722A  pdb=" N   LEU C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   TYR C 229 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA C 231 " --> pdb=" O   ASP C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 245
    Processing helix  chain 'C' and resid 250 through 267
      removed outlier: 3.507A  pdb=" N   LEU C 254 " --> pdb=" O   ASP C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 280
      removed outlier: 3.539A  pdb=" N   LEU C 280 " --> pdb=" O   LEU C 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 19
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 36 through 49
    Processing helix  chain 'E' and resid 53 through 55
      No H-bonds generated for 'chain 'E' and resid 53 through 55'
    Processing helix  chain 'E' and resid 68 through 77
    Processing helix  chain 'E' and resid 86 through 89
    Processing helix  chain 'E' and resid 97 through 101
    Processing helix  chain 'E' and resid 102 through 114
      removed outlier: 3.999A  pdb=" N   ASN E 114 " --> pdb=" O   GLU E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 129
      removed outlier: 3.581A  pdb=" N   ARG E 118 " --> pdb=" O   ASN E 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 205
    Processing helix  chain 'E' and resid 219 through 231
      removed outlier: 3.806A  pdb=" N   LEU E 228 " --> pdb=" O   ASP E 224 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   TYR E 229 " --> pdb=" O   VAL E 225 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   ALA E 231 " --> pdb=" O   ASP E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 245
    Processing helix  chain 'E' and resid 250 through 265
      removed outlier: 4.451A  pdb=" N   ASP E 265 " --> pdb=" O   ASP E 261 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 266 through 280
      removed outlier: 3.648A  pdb=" N   LEU E 280 " --> pdb=" O   LEU E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 298 through 303
    Processing helix  chain 'F' and resid 51 through 53
      No H-bonds generated for 'chain 'F' and resid 51 through 53'
    Processing helix  chain 'F' and resid 68 through 78
    Processing helix  chain 'F' and resid 102 through 114
      removed outlier: 3.881A  pdb=" N   ASN F 114 " --> pdb=" O   GLU F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 114 through 130
    Processing helix  chain 'F' and resid 139 through 163
    Processing helix  chain 'F' and resid 180 through 205
    Processing helix  chain 'F' and resid 219 through 231
      removed outlier: 3.758A  pdb=" N   LEU F 228 " --> pdb=" O   ASP F 224 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   TYR F 229 " --> pdb=" O   VAL F 225 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ALA F 231 " --> pdb=" O   ASP F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 245
    Processing helix  chain 'F' and resid 250 through 267
    Processing helix  chain 'F' and resid 267 through 280
      removed outlier: 3.868A  pdb=" N   LEU F 280 " --> pdb=" O   LEU F 276 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27
      removed outlier: 5.798A  pdb=" N   GLU A  25 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL A  32 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ALA A  27 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   MET A   3 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ALA A  61 " --> pdb=" O   MET A   3 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A  56 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 5.461A  pdb=" N   ILE A  88 " --> pdb=" O   ARG F  49 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ARG F  49 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291
      removed outlier: 8.105A  pdb=" N   VAL B  57 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR B  23 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU B  59 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   ILE B  25 " --> pdb=" O   LEU B  59 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU B  58 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   VAL B  84 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   LEU B  60 " --> pdb=" O   VAL B  84 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   SER B  94 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   TRP B  83 " --> pdb=" O   TYR B  92 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   TYR C  91 " --> pdb=" O   TRP C  83 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR C  23 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   LEU C  59 " --> pdb=" O   THR C  23 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE C  25 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310
      removed outlier: 3.901A  pdb=" N   ASN B 308 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ARG C  34 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ARG C  49 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   ILE D  88 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215
    Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27
      removed outlier: 7.287A  pdb=" N   VAL D  30 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   MET D   3 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA D  61 " --> pdb=" O   MET D   3 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291
      removed outlier: 7.715A  pdb=" N   VAL E  57 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   THR E  23 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   LEU E  59 " --> pdb=" O   THR E  23 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ILE E  25 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR F  91 " --> pdb=" O   TRP F  83 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   THR F  23 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   LEU F  59 " --> pdb=" O   THR F  23 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ILE F  25 " --> pdb=" O   LEU F  59 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310
      removed outlier: 7.598A  pdb=" N   ILE E  32 " --> pdb=" O   SER E  67 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1638 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      47 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 3.93

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3360
        1.34 -     1.45: 2039
        1.45 -     1.57: 6193
        1.57 -     1.69: 114
        1.69 -     1.81: 60
  Bond restraints: 11766
  Sorted by residual:
  bond pdb=" CB  ILE A  26 "
       pdb=" CG2 ILE A  26 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  bond pdb=" C3'  DC G   8 "
       pdb=" O3'  DC G   8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.36e+00
  bond pdb=" C4'  DG G  24 "
       pdb=" O4'  DG G  24 "
    ideal  model  delta    sigma   weight residual
    1.450  1.431  0.019 2.00e-02 2.50e+03 9.49e-01
  bond pdb=" C3'  DT H   9 "
       pdb=" C2'  DT H   9 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 8.78e-01
  bond pdb=" CA  GLN C  87 "
       pdb=" CB  GLN C  87 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.015 1.70e-02 3.46e+03 7.95e-01
  ... (remaining 11761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 15632
        1.20 -     2.41: 432
        2.41 -     3.61: 87
        3.61 -     4.81: 12
        4.81 -     6.02: 11
  Bond angle restraints: 16174
  Sorted by residual:
  angle pdb=" CA  GLN C  87 "
        pdb=" CB  GLN C  87 "
        pdb=" CG  GLN C  87 "
      ideal   model   delta    sigma   weight residual
     114.10  119.22   -5.12 2.00e+00 2.50e-01 6.55e+00
  angle pdb=" CA  GLN F  87 "
        pdb=" CB  GLN F  87 "
        pdb=" CG  GLN F  87 "
      ideal   model   delta    sigma   weight residual
     114.10  118.53   -4.43 2.00e+00 2.50e-01 4.90e+00
  angle pdb=" C   ALA E  99 "
        pdb=" N   ARG E 100 "
        pdb=" CA  ARG E 100 "
      ideal   model   delta    sigma   weight residual
     121.54  125.35   -3.81 1.91e+00 2.74e-01 3.97e+00
  angle pdb=" N   VAL E  35 "
        pdb=" CA  VAL E  35 "
        pdb=" C   VAL E  35 "
      ideal   model   delta    sigma   weight residual
     109.17  106.16    3.01 1.54e+00 4.22e-01 3.81e+00
  angle pdb=" CA  GLY B 179 "
        pdb=" C   GLY B 179 "
        pdb=" N   ASP B 180 "
      ideal   model   delta    sigma   weight residual
     114.48  116.79   -2.31 1.19e+00 7.06e-01 3.77e+00
  ... (remaining 16169 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.99: 6645
       35.99 -    71.98: 279
       71.98 -   107.97: 9
      107.97 -   143.96: 0
      143.96 -   179.96: 1
  Dihedral angle restraints: 6934
    sinusoidal: 3177
      harmonic: 3757
  Sorted by residual:
  dihedral pdb=" C4'  DC G   8 "
           pdb=" C3'  DC G   8 "
           pdb=" O3'  DC G   8 "
           pdb=" P    DT G   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.96 -179.96     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  ARG E  34 "
           pdb=" C   ARG E  34 "
           pdb=" N   VAL E  35 "
           pdb=" CA  VAL E  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  GLU F  19 "
           pdb=" C   GLU F  19 "
           pdb=" N   ASP F  20 "
           pdb=" CA  ASP F  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.21  -18.79     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 6931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1317
       0.037 -    0.074: 375
       0.074 -    0.110: 100
       0.110 -    0.147: 29
       0.147 -    0.184: 2
  Chirality restraints: 1823
  Sorted by residual:
  chirality pdb=" CB  VAL C 191 "
            pdb=" CA  VAL C 191 "
            pdb=" CG1 VAL C 191 "
            pdb=" CG2 VAL C 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.44e-01
  chirality pdb=" CA  ILE B  50 "
            pdb=" N   ILE B  50 "
            pdb=" C   ILE B  50 "
            pdb=" CB  ILE B  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CB  THR E 113 "
            pdb=" CA  THR E 113 "
            pdb=" OG1 THR E 113 "
            pdb=" CG2 THR E 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1820 not shown)

  Planarity restraints: 1879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 172 "   -0.025 5.00e-02 4.00e+02   3.91e-02 2.44e+00
        pdb=" N   PRO B 173 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D  85 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO D  86 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D  86 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D  86 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  31 "   -0.009 2.00e-02 2.50e+03   9.37e-03 1.76e+00
        pdb=" CG  TYR A  31 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  31 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  31 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  31 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  31 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  31 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1876 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 492
        2.72 -     3.26: 11148
        3.26 -     3.81: 20453
        3.81 -     4.35: 25083
        4.35 -     4.90: 41575
  Nonbonded interactions: 98751
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 229 "
            pdb=" OD2 ASP F 275 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR E 229 "
            pdb=" OD2 ASP E 275 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG1 THR A   7 "
            pdb=" OG  SER A  57 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   LEU E 295 "
            pdb=" OH  TYR E 309 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   GLY D  17 "
            pdb=" OG1 THR D  20 "
     model   vdw
     2.213 3.040
  ... (remaining 98746 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 283)
  selection = (chain 'C' and resid 20 through 283)
  selection = (chain 'F' and resid 20 through 283)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.150
  Process input model:                     33.560
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  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:11.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11766  Z= 0.134
  Angle     :  0.511   6.016  16174  Z= 0.279
  Chirality :  0.040   0.184   1823
  Planarity :  0.003   0.047   1879
  Dihedral  : 16.989 179.956   4524
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.24), residues: 1288
  helix:  2.15 (0.21), residues: 601
  sheet:  0.05 (0.40), residues: 201
  loop : -0.49 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  83 
 HIS   0.010   0.001   HIS B  29 
 PHE   0.008   0.001   PHE A  35 
 TYR   0.022   0.001   TYR A  31 
 ARG   0.008   0.000   ARG F 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16746 (  621)
  hydrogen bonds       : angle       6.58993 ( 1724)
  covalent geometry    : bond        0.00299 (11766)
  covalent geometry    : angle       0.51095 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 1.088 
Fit side-chains
REVERT: A   58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp)
REVERT: C  257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp)
REVERT: F  254 LEU cc_start: 0.8294 (tt) cc_final: 0.8082 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 244
  average time/residue: 1.1998
  time to fit residues: 316.5988
Evaluate side-chains
  181 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  254 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 54 optimal weight:    0.3980
   chunk 105 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
C  33 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.125032 restraints weight = 12287.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.75
r_work: 0.3327 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11766  Z= 0.192
  Angle     :  0.575   7.525  16174  Z= 0.313
  Chirality :  0.043   0.174   1823
  Planarity :  0.004   0.038   1879
  Dihedral  : 18.489 176.845   2097
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.29 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1288
  helix:  2.08 (0.21), residues: 608
  sheet: -0.21 (0.38), residues: 206
  loop : -0.57 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.013   0.001   HIS B  29 
 PHE   0.014   0.001   PHE D  89 
 TYR   0.016   0.001   TYR A  31 
 ARG   0.006   0.000   ARG C 258 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04924 (  621)
  hydrogen bonds       : angle       4.67889 ( 1724)
  covalent geometry    : bond        0.00446 (11766)
  covalent geometry    : angle       0.57516 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 1.223 
Fit side-chains
REVERT: B  302 LEU cc_start: 0.8313 (mt) cc_final: 0.8070 (mm)
REVERT: C  128 MET cc_start: 0.7562 (mtm) cc_final: 0.7340 (mtm)
REVERT: C  257 LEU cc_start: 0.8287 (tt) cc_final: 0.7930 (tp)
REVERT: D   10 ASN cc_start: 0.7398 (t0) cc_final: 0.7094 (m-40)
REVERT: E   31 LYS cc_start: 0.8168 (mtpm) cc_final: 0.7695 (mttp)
REVERT: E  244 GLU cc_start: 0.7685 (tt0) cc_final: 0.7363 (tt0)
REVERT: E  289 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5431 (pp20)
  outliers start: 30
  outliers final: 14
  residues processed: 208
  average time/residue: 1.1324
  time to fit residues: 256.7020
Evaluate side-chains
  184 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 108 optimal weight:    0.4980
   chunk 128 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
C 308 ASN
D  48 GLN
E  29 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.157979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126525 restraints weight = 12407.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.75
r_work: 0.3342 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11766  Z= 0.152
  Angle     :  0.523   6.695  16174  Z= 0.286
  Chirality :  0.041   0.162   1823
  Planarity :  0.004   0.035   1879
  Dihedral  : 18.453 177.979   2095
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.98 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1288
  helix:  2.24 (0.21), residues: 610
  sheet: -0.19 (0.37), residues: 201
  loop : -0.58 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 296 
 HIS   0.009   0.001   HIS B  29 
 PHE   0.011   0.001   PHE D  89 
 TYR   0.013   0.001   TYR D  31 
 ARG   0.005   0.000   ARG F  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  621)
  hydrogen bonds       : angle       4.40172 ( 1724)
  covalent geometry    : bond        0.00350 (11766)
  covalent geometry    : angle       0.52300 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9073 (ttp) cc_final: 0.8669 (ttp)
REVERT: C   17 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7600 (mtm-85)
REVERT: C  128 MET cc_start: 0.7635 (mtm) cc_final: 0.7410 (mtm)
REVERT: C  257 LEU cc_start: 0.8382 (tt) cc_final: 0.8016 (tp)
REVERT: C  263 PHE cc_start: 0.7878 (m-10) cc_final: 0.7662 (m-10)
REVERT: D   23 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8576 (ptm)
REVERT: E   31 LYS cc_start: 0.8109 (mtpm) cc_final: 0.7784 (mtpp)
REVERT: E   33 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7525 (m-40)
REVERT: E  244 GLU cc_start: 0.7632 (tt0) cc_final: 0.7355 (tt0)
REVERT: E  270 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7603 (mtpt)
REVERT: F  138 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6053 (tt)
REVERT: F  253 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7869 (tm-30)
  outliers start: 42
  outliers final: 17
  residues processed: 207
  average time/residue: 1.2157
  time to fit residues: 272.6546
Evaluate side-chains
  196 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   37 SER
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 131 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
C 308 ASN
E  29 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126458 restraints weight = 12365.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.75
r_work: 0.3338 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11766  Z= 0.149
  Angle     :  0.517   6.774  16174  Z= 0.282
  Chirality :  0.041   0.163   1823
  Planarity :  0.003   0.033   1879
  Dihedral  : 18.500 177.680   2095
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 14.73 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.24), residues: 1288
  helix:  2.31 (0.21), residues: 610
  sheet: -0.25 (0.37), residues: 201
  loop : -0.52 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.008   0.001   HIS B  29 
 PHE   0.011   0.001   PHE D  89 
 TYR   0.009   0.001   TYR B 194 
 ARG   0.006   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  621)
  hydrogen bonds       : angle       4.27469 ( 1724)
  covalent geometry    : bond        0.00343 (11766)
  covalent geometry    : angle       0.51715 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 189
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9071 (ttp) cc_final: 0.8667 (ttp)
REVERT: B  152 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8020 (ttm170)
REVERT: B  172 ASN cc_start: 0.8744 (t0) cc_final: 0.8374 (t0)
REVERT: B  302 LEU cc_start: 0.8298 (mt) cc_final: 0.8085 (mm)
REVERT: C   17 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7595 (mtm-85)
REVERT: C  232 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7631 (pp20)
REVERT: C  257 LEU cc_start: 0.8380 (tt) cc_final: 0.8127 (tp)
REVERT: C  263 PHE cc_start: 0.7863 (m-10) cc_final: 0.7640 (m-10)
REVERT: D    3 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7698 (ttt)
REVERT: D   23 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8520 (ptm)
REVERT: E   31 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7812 (mttm)
REVERT: E   33 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7524 (m-40)
REVERT: E  244 GLU cc_start: 0.7650 (tt0) cc_final: 0.7343 (tt0)
REVERT: E  270 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7649 (mtpt)
REVERT: E  289 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5510 (pp20)
REVERT: F  138 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6055 (tt)
REVERT: F  253 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7871 (tm-30)
REVERT: F  281 GLU cc_start: 0.8572 (mp0) cc_final: 0.8299 (mp0)
  outliers start: 43
  outliers final: 23
  residues processed: 212
  average time/residue: 1.1936
  time to fit residues: 274.5071
Evaluate side-chains
  200 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   34 ASN
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue   37 SER
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 109 optimal weight:    0.3980
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
D  10 ASN
E  29 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.126016 restraints weight = 12325.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.79
r_work: 0.3335 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11766  Z= 0.154
  Angle     :  0.518   6.422  16174  Z= 0.282
  Chirality :  0.041   0.167   1823
  Planarity :  0.004   0.047   1879
  Dihedral  : 18.545 177.681   2095
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.14 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.24), residues: 1288
  helix:  2.33 (0.21), residues: 610
  sheet: -0.29 (0.36), residues: 201
  loop : -0.52 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.007   0.001   HIS B  29 
 PHE   0.010   0.001   PHE D  89 
 TYR   0.014   0.001   TYR F 223 
 ARG   0.008   0.000   ARG F 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  621)
  hydrogen bonds       : angle       4.22554 ( 1724)
  covalent geometry    : bond        0.00356 (11766)
  covalent geometry    : angle       0.51825 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 184
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9085 (ttp) cc_final: 0.8652 (ttp)
REVERT: B  172 ASN cc_start: 0.8727 (t0) cc_final: 0.8327 (t0)
REVERT: B  302 LEU cc_start: 0.8262 (mt) cc_final: 0.8007 (mm)
REVERT: C   17 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7558 (mtm-85)
REVERT: C  232 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7466 (pp20)
REVERT: D    3 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7655 (ttt)
REVERT: D   23 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8535 (ptm)
REVERT: E   31 LYS cc_start: 0.8067 (mtpm) cc_final: 0.7702 (mttm)
REVERT: E   33 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7511 (m-40)
REVERT: E  244 GLU cc_start: 0.7593 (tt0) cc_final: 0.7306 (tt0)
REVERT: E  270 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7498 (mtpt)
REVERT: E  289 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5413 (pp20)
REVERT: E  291 GLU cc_start: 0.7423 (tp30) cc_final: 0.7023 (tt0)
REVERT: F   72 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7709 (tt0)
REVERT: F  138 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6046 (tt)
  outliers start: 39
  outliers final: 22
  residues processed: 204
  average time/residue: 1.1910
  time to fit residues: 263.9009
Evaluate side-chains
  209 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 180
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   72 GLU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 94 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0980
   chunk 116 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 GLN
** C  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.154771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.122624 restraints weight = 12496.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.79
r_work: 0.3291 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11766  Z= 0.210
  Angle     :  0.567   6.241  16174  Z= 0.306
  Chirality :  0.043   0.201   1823
  Planarity :  0.004   0.033   1879
  Dihedral  : 18.702 177.678   2095
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.70 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1288
  helix:  2.16 (0.20), residues: 610
  sheet: -0.51 (0.35), residues: 211
  loop : -0.55 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 296 
 HIS   0.008   0.001   HIS B  29 
 PHE   0.012   0.002   PHE D  89 
 TYR   0.016   0.002   TYR F 223 
 ARG   0.006   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  621)
  hydrogen bonds       : angle       4.32572 ( 1724)
  covalent geometry    : bond        0.00494 (11766)
  covalent geometry    : angle       0.56738 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.7787 (tt0) cc_final: 0.7395 (tp30)
REVERT: A   58 MET cc_start: 0.9134 (ttp) cc_final: 0.8646 (ttp)
REVERT: B   33 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8080 (m-40)
REVERT: B  172 ASN cc_start: 0.8778 (t0) cc_final: 0.8405 (t0)
REVERT: C   17 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7536 (mtm-85)
REVERT: C  126 TYR cc_start: 0.7879 (t80) cc_final: 0.7632 (t80)
REVERT: C  232 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7734 (pp20)
REVERT: D   23 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8595 (ptm)
REVERT: D   35 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7890 (m-80)
REVERT: E   31 LYS cc_start: 0.8094 (mtpm) cc_final: 0.7681 (mttm)
REVERT: E   33 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7473 (m-40)
REVERT: E  244 GLU cc_start: 0.7482 (tt0) cc_final: 0.7234 (tt0)
REVERT: E  270 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7534 (mtpt)
REVERT: E  289 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5592 (pp20)
REVERT: E  291 GLU cc_start: 0.7462 (tp30) cc_final: 0.7041 (tt0)
REVERT: F   72 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7669 (tt0)
REVERT: F  103 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7749 (ptm160)
REVERT: F  138 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6001 (tt)
  outliers start: 43
  outliers final: 25
  residues processed: 200
  average time/residue: 1.1949
  time to fit residues: 258.5756
Evaluate side-chains
  203 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   34 ASN
Chi-restraints excluded: chain B residue   33 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  232 GLU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   35 PHE
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain E residue  289 GLU
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   72 GLU
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  102 THR
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 117 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0170
   chunk 58 optimal weight:    0.3980
   chunk 104 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0370
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.159174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127750 restraints weight = 12477.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.76
r_work: 0.3358 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11766  Z= 0.128
  Angle     :  0.513   6.680  16174  Z= 0.279
  Chirality :  0.041   0.170   1823
  Planarity :  0.003   0.032   1879
  Dihedral  : 18.503 177.132   2095
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.20 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1288
  helix:  2.32 (0.21), residues: 610
  sheet: -0.37 (0.36), residues: 207
  loop : -0.49 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 296 
 HIS   0.005   0.001   HIS B  29 
 PHE   0.008   0.001   PHE D  89 
 TYR   0.016   0.001   TYR F 223 
 ARG   0.007   0.000   ARG C 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  621)
  hydrogen bonds       : angle       4.17462 ( 1724)
  covalent geometry    : bond        0.00286 (11766)
  covalent geometry    : angle       0.51252 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 188
  time to evaluate  : 1.124 
Fit side-chains
REVERT: A   58 MET cc_start: 0.9099 (ttp) cc_final: 0.8657 (ttp)
REVERT: B  172 ASN cc_start: 0.8751 (t0) cc_final: 0.8378 (t0)
REVERT: C   17 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7534 (mtm-85)
REVERT: C  126 TYR cc_start: 0.7969 (t80) cc_final: 0.7726 (t80)
REVERT: C  232 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7758 (pp20)
REVERT: D    3 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7773 (tpp)
REVERT: D   23 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8512 (ptm)
REVERT: E   31 LYS cc_start: 0.8113 (mtpm) cc_final: 0.7888 (mtmm)
REVERT: E   33 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7470 (m-40)
REVERT: E  270 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7556 (mtpt)
REVERT: E  291 GLU cc_start: 0.7415 (tp30) cc_final: 0.7045 (tt0)
REVERT: F   23 THR cc_start: 0.8510 (m) cc_final: 0.8298 (p)
REVERT: F  103 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7667 (ptm160)
  outliers start: 38
  outliers final: 19
  residues processed: 210
  average time/residue: 1.2334
  time to fit residues: 280.2619
Evaluate side-chains
  202 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   40 THR
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   chunk 94 optimal weight:    0.1980
   chunk 55 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
E  29 HIS
F  33 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.158269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.126829 restraints weight = 12452.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.75
r_work: 0.3341 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11766  Z= 0.146
  Angle     :  0.528   6.446  16174  Z= 0.286
  Chirality :  0.042   0.243   1823
  Planarity :  0.004   0.031   1879
  Dihedral  : 18.504 177.197   2095
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.95 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.24), residues: 1288
  helix:  2.30 (0.21), residues: 609
  sheet: -0.37 (0.36), residues: 207
  loop : -0.52 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 296 
 HIS   0.006   0.001   HIS B  29 
 PHE   0.011   0.001   PHE F 263 
 TYR   0.016   0.001   TYR F 223 
 ARG   0.007   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  621)
  hydrogen bonds       : angle       4.18322 ( 1724)
  covalent geometry    : bond        0.00332 (11766)
  covalent geometry    : angle       0.52790 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.7671 (tt0) cc_final: 0.7399 (tp30)
REVERT: A   58 MET cc_start: 0.9119 (ttp) cc_final: 0.8674 (ttp)
REVERT: B  172 ASN cc_start: 0.8754 (t0) cc_final: 0.8363 (t0)
REVERT: C   17 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7530 (mtm-85)
REVERT: C  118 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7530 (ttt-90)
REVERT: C  126 TYR cc_start: 0.8000 (t80) cc_final: 0.7774 (t80)
REVERT: C  232 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7750 (pp20)
REVERT: D    3 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7598 (ttt)
REVERT: D   23 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8564 (ptm)
REVERT: E   31 LYS cc_start: 0.8061 (mtpm) cc_final: 0.7833 (mtmm)
REVERT: E   33 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7477 (m-40)
REVERT: E  270 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7534 (mtpt)
REVERT: E  291 GLU cc_start: 0.7361 (tp30) cc_final: 0.6988 (tt0)
REVERT: F  103 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7709 (ptm160)
  outliers start: 33
  outliers final: 20
  residues processed: 204
  average time/residue: 1.2045
  time to fit residues: 267.1724
Evaluate side-chains
  206 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0870
   chunk 84 optimal weight:    0.9980
   chunk 124 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:    0.6980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.158859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.127371 restraints weight = 12400.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.76
r_work: 0.3346 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11766  Z= 0.140
  Angle     :  0.531   6.805  16174  Z= 0.287
  Chirality :  0.041   0.203   1823
  Planarity :  0.004   0.035   1879
  Dihedral  : 18.481 176.973   2095
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.23 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.24), residues: 1288
  helix:  2.31 (0.21), residues: 607
  sheet: -0.38 (0.36), residues: 207
  loop : -0.51 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.006   0.001   HIS B  29 
 PHE   0.009   0.001   PHE D  89 
 TYR   0.016   0.001   TYR F 223 
 ARG   0.007   0.000   ARG C 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  621)
  hydrogen bonds       : angle       4.16977 ( 1724)
  covalent geometry    : bond        0.00319 (11766)
  covalent geometry    : angle       0.53087 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.9093 (ttp) cc_final: 0.8649 (ttp)
REVERT: B   33 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (m-40)
REVERT: B  172 ASN cc_start: 0.8641 (t0) cc_final: 0.8265 (t0)
REVERT: C   17 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7518 (mtm-85)
REVERT: C  118 ARG cc_start: 0.7870 (ttt-90) cc_final: 0.7497 (ttt-90)
REVERT: C  126 TYR cc_start: 0.7954 (t80) cc_final: 0.7724 (t80)
REVERT: C  232 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7675 (pp20)
REVERT: D    3 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7583 (ttt)
REVERT: D   23 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8551 (ptm)
REVERT: E   31 LYS cc_start: 0.8050 (mtpm) cc_final: 0.7817 (mtmm)
REVERT: E   33 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7469 (m-40)
REVERT: E  270 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7417 (mtpt)
REVERT: E  291 GLU cc_start: 0.7458 (tp30) cc_final: 0.7114 (tt0)
REVERT: F   23 THR cc_start: 0.8468 (m) cc_final: 0.8260 (p)
REVERT: F  103 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7747 (ptm160)
  outliers start: 35
  outliers final: 21
  residues processed: 201
  average time/residue: 1.1182
  time to fit residues: 244.8603
Evaluate side-chains
  203 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain B residue   33 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 76 optimal weight:    0.4980
   chunk 112 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 133 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  74 ASN
E  29 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.158214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126723 restraints weight = 12350.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.74
r_work: 0.3341 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11766  Z= 0.149
  Angle     :  0.544   7.557  16174  Z= 0.293
  Chirality :  0.042   0.222   1823
  Planarity :  0.004   0.032   1879
  Dihedral  : 18.492 176.978   2095
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.45 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.24), residues: 1288
  helix:  2.23 (0.21), residues: 607
  sheet: -0.42 (0.36), residues: 207
  loop : -0.53 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.006   0.001   HIS B  29 
 PHE   0.009   0.001   PHE D  89 
 TYR   0.015   0.001   TYR F 223 
 ARG   0.007   0.000   ARG C 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  621)
  hydrogen bonds       : angle       4.20628 ( 1724)
  covalent geometry    : bond        0.00343 (11766)
  covalent geometry    : angle       0.54449 (16174)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 GLU cc_start: 0.7665 (tt0) cc_final: 0.7394 (tp30)
REVERT: A   58 MET cc_start: 0.9104 (ttp) cc_final: 0.8654 (ttp)
REVERT: A   73 GLU cc_start: 0.7040 (tt0) cc_final: 0.6827 (tt0)
REVERT: B   33 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8115 (m-40)
REVERT: B  172 ASN cc_start: 0.8645 (t0) cc_final: 0.8300 (t0)
REVERT: C   17 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7547 (mtm-85)
REVERT: C  118 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7508 (ttt-90)
REVERT: C  126 TYR cc_start: 0.7931 (t80) cc_final: 0.7714 (t80)
REVERT: C  232 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7752 (pp20)
REVERT: D    3 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7654 (ttt)
REVERT: D   23 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8524 (ptm)
REVERT: E   31 LYS cc_start: 0.8069 (mtpm) cc_final: 0.7786 (mtpp)
REVERT: E   33 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7476 (m-40)
REVERT: E  270 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7441 (mtpt)
REVERT: E  291 GLU cc_start: 0.7417 (tp30) cc_final: 0.7112 (tt0)
REVERT: F   23 THR cc_start: 0.8498 (m) cc_final: 0.8263 (p)
  outliers start: 29
  outliers final: 19
  residues processed: 198
  average time/residue: 1.1129
  time to fit residues: 241.2679
Evaluate side-chains
  203 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 GLU
Chi-restraints excluded: chain B residue   33 ASN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue  170 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   65 ASP
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain D residue    3 MET
Chi-restraints excluded: chain D residue   23 MET
Chi-restraints excluded: chain E residue   33 ASN
Chi-restraints excluded: chain E residue   35 VAL
Chi-restraints excluded: chain E residue  101 SER
Chi-restraints excluded: chain E residue  207 SER
Chi-restraints excluded: chain F residue    5 ILE
Chi-restraints excluded: chain F residue   18 VAL
Chi-restraints excluded: chain F residue   35 VAL
Chi-restraints excluded: chain F residue   55 ILE
Chi-restraints excluded: chain F residue   98 LEU
Chi-restraints excluded: chain F residue  140 MET
Chi-restraints excluded: chain F residue  234 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 121 optimal weight:    0.3980
   chunk 12 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.158647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.128415 restraints weight = 12359.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.73
r_work: 0.3334 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11766  Z= 0.146
  Angle     :  0.548   7.623  16174  Z= 0.294
  Chirality :  0.042   0.209   1823
  Planarity :  0.004   0.049   1879
  Dihedral  : 18.479 176.809   2095
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.45 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.24), residues: 1288
  helix:  2.21 (0.21), residues: 606
  sheet: -0.43 (0.36), residues: 207
  loop : -0.51 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 296 
 HIS   0.006   0.001   HIS B  29 
 PHE   0.009   0.001   PHE D  89 
 TYR   0.015   0.001   TYR F 223 
 ARG   0.007   0.000   ARG C 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04302 (  621)
  hydrogen bonds       : angle       4.20531 ( 1724)
  covalent geometry    : bond        0.00334 (11766)
  covalent geometry    : angle       0.54771 (16174)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8309.49 seconds
wall clock time: 143 minutes 54.36 seconds (8634.36 seconds total)