Starting phenix.real_space_refine
on Wed Jan 15 16:46:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fab_50271/01_2025/9fab_50271_trim.cif"
  }
  resolution = 3.9
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2770      2.51       5
     N     725      2.21       5
     O     900      1.98       5
     H    4190      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8595
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.12, per 1000 atoms: 0.48
  Number of scatterers: 8595
  At special positions: 0
  Unit cell: (91.567, 114.681, 44.45, 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      10     16.00
     O     900      8.00
     N     725      7.00
     C    2770      6.00
     H    4190      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A 201 " - " ASN A  19 "
      " NAG B 201 " - " ASN B  19 "
      " NAG C 201 " - " ASN C  19 "
      " NAG D 201 " - " ASN D  19 "
      " NAG E 201 " - " ASN E  19 "
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 700.2 milliseconds
  

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 5
      removed outlier: 6.295A  pdb=" N   GLU B   3 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   GLU A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12
      removed outlier: 6.378A  pdb=" N   SER B   9 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   VAL D  12 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   SER B  11 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   SER A   9 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL B  12 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   SER A  11 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23
      removed outlier: 6.872A  pdb=" N   THR B  17 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   ILE D  20 " --> pdb=" O   THR B  17 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   ASN B  19 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   CYS D  22 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   THR B  21 " --> pdb=" O   CYS D  22 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   THR A  17 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 8.192A  pdb=" N   ILE B  20 " --> pdb=" O   THR A  17 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ASN A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 8.258A  pdb=" N   CYS B  22 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   THR A  21 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA A  18 " --> pdb=" O   ASN C  19 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   THR C  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE A  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   SER C  23 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   CYS A  22 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30
      removed outlier: 6.181A  pdb=" N   TYR B  26 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   GLU D  29 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   GLY B  28 " --> pdb=" O   GLU D  29 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   TYR A  26 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   GLU B  29 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLY A  28 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 37
      removed outlier: 6.266A  pdb=" N   SER B  33 " --> pdb=" O   TRP D  34 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   GLN D  36 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   TYR B  35 " --> pdb=" O   GLN D  36 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   SER A  33 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   GLN B  36 " --> pdb=" O   SER A  33 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   TYR A  35 " --> pdb=" O   GLN B  36 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 52
      removed outlier: 6.787A  pdb=" N   VAL B  44 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   ILE D  47 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL B  46 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   GLN D  49 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   TYR B  48 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   SER D  51 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   SER B  50 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   VAL A  44 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   ILE B  47 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL A  46 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   GLN B  49 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR A  48 " --> pdb=" O   GLN B  49 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   SER B  51 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   SER A  50 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75
      removed outlier: 6.507A  pdb=" N   THR B  73 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   THR A  73 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86
      removed outlier: 6.879A  pdb=" N   ALA B  83 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   PHE D  86 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TYR B  85 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA A  83 " --> pdb=" O   ASP B  84 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   PHE B  86 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   TYR A  85 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 97
      removed outlier: 7.095A  pdb=" N   PHE B  97 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   PHE A  97 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   TRP A  90 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   THR C  93 " --> pdb=" O   TRP A  90 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   PHE A  92 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   VAL C  95 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   SER A  94 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   PHE C  97 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL A  96 " --> pdb=" O   PHE C  97 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   TRP C  90 " --> pdb=" O   ASP E  91 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   THR E  93 " --> pdb=" O   TRP C  90 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   PHE C  92 " --> pdb=" O   THR E  93 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   VAL E  95 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   SER C  94 " --> pdb=" O   VAL E  95 " (cutoff:3.500A)
      removed outlier: 7.700A  pdb=" N   PHE E  97 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   VAL C  96 " --> pdb=" O   PHE E  97 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 102 through 103
      removed outlier: 6.183A  pdb=" N   LYS B 102 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LYS A 102 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 114 through 116
      removed outlier: 6.315A  pdb=" N   VAL A 115 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL C 115 " --> pdb=" O   THR E 116 " (cutoff:3.500A)

    82 hydrogen bonds defined for protein.
    243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 4190
        1.04 -     1.24: 655
        1.24 -     1.45: 1368
        1.45 -     1.65: 2482
        1.65 -     1.86: 10
  Bond restraints: 8705
  Sorted by residual:
  bond pdb=" CA  THR A  21 "
       pdb=" C   THR A  21 "
    ideal  model  delta    sigma   weight residual
    1.521  1.542 -0.021 1.26e-02 6.30e+03 2.70e+00
  bond pdb=" CA  THR B  21 "
       pdb=" C   THR B  21 "
    ideal  model  delta    sigma   weight residual
    1.521  1.541 -0.021 1.26e-02 6.30e+03 2.65e+00
  bond pdb=" CA  THR C  21 "
       pdb=" C   THR C  21 "
    ideal  model  delta    sigma   weight residual
    1.521  1.541 -0.020 1.26e-02 6.30e+03 2.61e+00
  bond pdb=" CA  THR D  21 "
       pdb=" C   THR D  21 "
    ideal  model  delta    sigma   weight residual
    1.521  1.541 -0.020 1.26e-02 6.30e+03 2.60e+00
  bond pdb=" CA  THR E  21 "
       pdb=" C   THR E  21 "
    ideal  model  delta    sigma   weight residual
    1.521  1.541 -0.020 1.26e-02 6.30e+03 2.56e+00
  ... (remaining 8700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 14274
        1.95 -     3.89: 1141
        3.89 -     5.84: 185
        5.84 -     7.78: 40
        7.78 -     9.73: 10
  Bond angle restraints: 15650
  Sorted by residual:
  angle pdb=" N   THR B  77 "
        pdb=" CA  THR B  77 "
        pdb=" C   THR B  77 "
      ideal   model   delta    sigma   weight residual
     111.07  116.38   -5.31 1.07e+00 8.73e-01 2.46e+01
  angle pdb=" N   THR A  77 "
        pdb=" CA  THR A  77 "
        pdb=" C   THR A  77 "
      ideal   model   delta    sigma   weight residual
     111.07  116.35   -5.28 1.07e+00 8.73e-01 2.44e+01
  angle pdb=" N   THR C  77 "
        pdb=" CA  THR C  77 "
        pdb=" C   THR C  77 "
      ideal   model   delta    sigma   weight residual
     111.07  116.34   -5.27 1.07e+00 8.73e-01 2.43e+01
  angle pdb=" N   THR E  77 "
        pdb=" CA  THR E  77 "
        pdb=" C   THR E  77 "
      ideal   model   delta    sigma   weight residual
     111.07  116.31   -5.24 1.07e+00 8.73e-01 2.40e+01
  angle pdb=" N   THR D  77 "
        pdb=" CA  THR D  77 "
        pdb=" C   THR D  77 "
      ideal   model   delta    sigma   weight residual
     111.07  116.30   -5.23 1.07e+00 8.73e-01 2.39e+01
  ... (remaining 15645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.68: 3759
       14.68 -    29.37: 309
       29.37 -    44.05: 90
       44.05 -    58.73: 95
       58.73 -    73.42: 30
  Dihedral angle restraints: 4283
    sinusoidal: 2363
      harmonic: 1920
  Sorted by residual:
  dihedral pdb=" CA  THR A  69 "
           pdb=" C   THR A  69 "
           pdb=" N   ALA A  70 "
           pdb=" CA  ALA A  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  THR C  69 "
           pdb=" C   THR C  69 "
           pdb=" N   ALA C  70 "
           pdb=" CA  ALA C  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  THR D  69 "
           pdb=" C   THR D  69 "
           pdb=" N   ALA D  70 "
           pdb=" CA  ALA D  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.77  -17.23     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4280 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 309
       0.038 -    0.076: 209
       0.076 -    0.113: 94
       0.113 -    0.151: 58
       0.151 -    0.189: 30
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" C1  NAG D 201 "
            pdb=" ND2 ASN D  19 "
            pdb=" C2  NAG D 201 "
            pdb=" O5  NAG D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.91e-01
  chirality pdb=" C1  NAG C 201 "
            pdb=" ND2 ASN C  19 "
            pdb=" C2  NAG C 201 "
            pdb=" O5  NAG C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" C1  NAG A 201 "
            pdb=" ND2 ASN A  19 "
            pdb=" C2  NAG A 201 "
            pdb=" O5  NAG A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 697 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  90 "   -0.005 2.00e-02 2.50e+03   1.78e-02 1.27e+01
        pdb=" CG  TRP E  90 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  90 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  90 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  90 "    0.026 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  90 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  90 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  90 "    0.015 2.00e-02 2.50e+03
        pdb=" HD1 TRP E  90 "    0.012 2.00e-02 2.50e+03
        pdb=" HE1 TRP E  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP E  90 "    0.011 2.00e-02 2.50e+03
        pdb=" HZ2 TRP E  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HZ3 TRP E  90 "   -0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP E  90 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  90 "   -0.005 2.00e-02 2.50e+03   1.78e-02 1.26e+01
        pdb=" CG  TRP C  90 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  90 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  90 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  90 "    0.027 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  90 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  90 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  90 "    0.014 2.00e-02 2.50e+03
        pdb=" HD1 TRP C  90 "    0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP C  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP C  90 "    0.011 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C  90 "   -0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP C  90 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  90 "   -0.005 2.00e-02 2.50e+03   1.77e-02 1.26e+01
        pdb=" CG  TRP D  90 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  90 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  90 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  90 "    0.027 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  90 "    0.016 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  90 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  90 "    0.014 2.00e-02 2.50e+03
        pdb=" HD1 TRP D  90 "    0.013 2.00e-02 2.50e+03
        pdb=" HE1 TRP D  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP D  90 "    0.010 2.00e-02 2.50e+03
        pdb=" HZ2 TRP D  90 "   -0.022 2.00e-02 2.50e+03
        pdb=" HZ3 TRP D  90 "   -0.000 2.00e-02 2.50e+03
        pdb=" HH2 TRP D  90 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        1.82 -     2.38: 3589
        2.38 -     2.93: 18474
        2.93 -     3.49: 19251
        3.49 -     4.04: 28985
        4.04 -     4.60: 40178
  Nonbonded interactions: 110477
  Sorted by model distance:
  nonbonded pdb=" O   THR B 104 "
            pdb=" HG1 THR B 104 "
     model   vdw
     1.824 2.450
  nonbonded pdb=" O   THR D 104 "
            pdb=" HG1 THR D 104 "
     model   vdw
     1.825 2.450
  nonbonded pdb=" O   THR A 104 "
            pdb=" HG1 THR A 104 "
     model   vdw
     1.825 2.450
  nonbonded pdb=" O   THR C 104 "
            pdb=" HG1 THR C 104 "
     model   vdw
     1.825 2.450
  nonbonded pdb=" O   THR E 104 "
            pdb=" HG1 THR E 104 "
     model   vdw
     1.825 2.450
  ... (remaining 110472 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.160
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.110
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
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      :  0.010   0.058   4515  Z= 0.690
  Angle     :  1.566   9.728   6160  Z= 0.923
  Chirality :  0.070   0.189    700
  Planarity :  0.007   0.051    795
  Dihedral  : 11.241  73.418   1675
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.50 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.009   TRP A  90 
 PHE   0.022   0.005   PHE A   2 
 TYR   0.040   0.008   TYR B  85 
 ARG   0.005   0.002   ARG E  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.8487 (mt) cc_final: 0.8181 (mt)
REVERT: A   78 GLN cc_start: 0.7987 (tt0) cc_final: 0.7777 (tt0)
REVERT: A  110 LYS cc_start: 0.7916 (tptm) cc_final: 0.7643 (mptt)
REVERT: A  115 VAL cc_start: 0.6206 (t) cc_final: 0.5965 (t)
REVERT: C   88 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: C  110 LYS cc_start: 0.8031 (tptm) cc_final: 0.7584 (mptt)
REVERT: D   38 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8316 (mmtt)
REVERT: D   78 GLN cc_start: 0.8016 (tt0) cc_final: 0.7484 (tp-100)
REVERT: E   36 GLN cc_start: 0.7393 (tt0) cc_final: 0.7024 (pm20)
REVERT: E   61 PHE cc_start: 0.5374 (p90) cc_final: 0.5058 (t80)
REVERT: E   72 LEU cc_start: 0.8601 (tp) cc_final: 0.8397 (pp)
REVERT: E   86 PHE cc_start: 0.6696 (m-80) cc_final: 0.6025 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.3081
  time to fit residues: 53.7184
Evaluate side-chains
  66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
C  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.152843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.135601 restraints weight = 25661.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.139872 restraints weight = 11443.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.142495 restraints weight = 6338.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4515  Z= 0.269
  Angle     :  0.721   4.946   6160  Z= 0.389
  Chirality :  0.049   0.217    700
  Planarity :  0.005   0.040    795
  Dihedral  :  6.109  19.381    725
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  9.07 %
    Favored  : 88.25 %
  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: -4.59 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E  34 
 PHE   0.017   0.002   PHE C   2 
 TYR   0.029   0.003   TYR A  31 
 ARG   0.004   0.001   ARG A  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7938 (tptm) cc_final: 0.7597 (mptt)
REVERT: C  110 LYS cc_start: 0.7982 (tptm) cc_final: 0.7529 (mptt)
REVERT: D   38 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8003 (mmtt)
REVERT: E   36 GLN cc_start: 0.7838 (tt0) cc_final: 0.7586 (pm20)
REVERT: E   86 PHE cc_start: 0.6503 (m-80) cc_final: 0.5774 (p90)
  outliers start: 13
  outliers final: 8
  residues processed: 90
  average time/residue: 0.2708
  time to fit residues: 32.1013
Evaluate side-chains
  65 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain E residue   88 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  68 ASN
A  78 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.151117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.134056 restraints weight = 26081.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.138186 restraints weight = 12005.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.140769 restraints weight = 6773.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4515  Z= 0.242
  Angle     :  0.630   4.099   6160  Z= 0.335
  Chirality :  0.047   0.205    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.107  27.266    725
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.13 %
    Favored  : 86.60 %
  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: -4.84 (0.21), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.68 (0.16), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  90 
 PHE   0.011   0.001   PHE A   2 
 TYR   0.014   0.002   TYR A  31 
 ARG   0.002   0.000   ARG E  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7861 (tptm) cc_final: 0.7561 (mptt)
REVERT: C  110 LYS cc_start: 0.7926 (tptm) cc_final: 0.7569 (mptt)
REVERT: D   38 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8172 (mmtt)
REVERT: E   86 PHE cc_start: 0.6226 (m-80) cc_final: 0.5598 (p90)
  outliers start: 11
  outliers final: 9
  residues processed: 67
  average time/residue: 0.2912
  time to fit residues: 25.6464
Evaluate side-chains
  64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain E residue   87 CYS
Chi-restraints excluded: chain E residue   88 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.151904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.134821 restraints weight = 25634.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.138971 restraints weight = 11894.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.141600 restraints weight = 6646.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4515  Z= 0.208
  Angle     :  0.575   3.844   6160  Z= 0.303
  Chirality :  0.046   0.180    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.218  30.887    725
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.34 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.91 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  90 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.010   0.002   TYR C  85 
 ARG   0.001   0.000   ARG E  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7833 (tptm) cc_final: 0.7567 (mptt)
REVERT: C  110 LYS cc_start: 0.7934 (tptm) cc_final: 0.7520 (mptt)
REVERT: D   38 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8047 (mmtt)
REVERT: E   86 PHE cc_start: 0.6254 (m-80) cc_final: 0.5641 (p90)
  outliers start: 12
  outliers final: 11
  residues processed: 67
  average time/residue: 0.2817
  time to fit residues: 24.8798
Evaluate side-chains
  64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   57 ILE
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   87 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    0.1980
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
D  41 GLN
D  68 ASN
E  68 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.150776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.133459 restraints weight = 25407.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.137763 restraints weight = 11447.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.140434 restraints weight = 6334.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4515  Z= 0.244
  Angle     :  0.589   5.584   6160  Z= 0.311
  Chirality :  0.047   0.183    700
  Planarity :  0.005   0.044    795
  Dihedral  :  6.776  37.915    725
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.55 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.09 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.87 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  90 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.013   0.002   TYR A  85 
 ARG   0.002   0.000   ARG D  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.624 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.7943 (tptm) cc_final: 0.7595 (mptt)
REVERT: D   38 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8149 (mmtt)
REVERT: E   86 PHE cc_start: 0.6332 (m-80) cc_final: 0.5482 (p90)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.3085
  time to fit residues: 26.0070
Evaluate side-chains
  61 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.0470
   chunk 34 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.9280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.151647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.134925 restraints weight = 25262.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.139074 restraints weight = 11556.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.141637 restraints weight = 6455.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4515  Z= 0.170
  Angle     :  0.533   4.816   6160  Z= 0.276
  Chirality :  0.046   0.159    700
  Planarity :  0.005   0.042    795
  Dihedral  :  5.959  30.181    725
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.99 %
    Favored  : 85.15 %
  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: -5.03 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  90 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.008   0.001   TYR A  85 
 ARG   0.001   0.000   ARG A  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.608 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.8063 (tptm) cc_final: 0.7657 (mptt)
REVERT: D   38 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8111 (mmtt)
REVERT: E   86 PHE cc_start: 0.6316 (m-80) cc_final: 0.5550 (p90)
  outliers start: 9
  outliers final: 8
  residues processed: 63
  average time/residue: 0.3051
  time to fit residues: 25.0945
Evaluate side-chains
  61 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   87 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 54 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.152084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.134834 restraints weight = 25471.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.139215 restraints weight = 11453.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.141933 restraints weight = 6337.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4515  Z= 0.179
  Angle     :  0.530   3.971   6160  Z= 0.275
  Chirality :  0.045   0.152    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.013  32.163    725
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.81 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.05 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  90 
 PHE   0.013   0.001   PHE C  86 
 TYR   0.009   0.001   TYR A  85 
 ARG   0.001   0.000   ARG D  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.649 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.8051 (tptm) cc_final: 0.7648 (mptt)
REVERT: D   38 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8142 (mmtt)
REVERT: E   86 PHE cc_start: 0.6425 (m-80) cc_final: 0.5537 (p90)
  outliers start: 8
  outliers final: 8
  residues processed: 58
  average time/residue: 0.3169
  time to fit residues: 24.4371
Evaluate side-chains
  59 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   87 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** 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 = 0.4493 r_free = 0.4493 target = 0.152332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.135368 restraints weight = 25092.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.139623 restraints weight = 11309.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.142238 restraints weight = 6259.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4515  Z= 0.185
  Angle     :  0.530   3.903   6160  Z= 0.275
  Chirality :  0.045   0.152    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.126  33.538    725
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.78 %
    Favored  : 84.74 %
  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: -5.11 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.89 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  90 
 PHE   0.013   0.001   PHE C  86 
 TYR   0.009   0.001   TYR A  85 
 ARG   0.002   0.000   ARG D  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.643 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.8070 (tptm) cc_final: 0.7698 (mptt)
REVERT: D   38 LYS cc_start: 0.8580 (mtmt) cc_final: 0.8168 (mmtt)
REVERT: E   86 PHE cc_start: 0.6420 (m-80) cc_final: 0.5543 (p90)
  outliers start: 12
  outliers final: 12
  residues processed: 59
  average time/residue: 0.2937
  time to fit residues: 22.8169
Evaluate side-chains
  63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain E residue   21 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0970
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** 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 = 0.4510 r_free = 0.4510 target = 0.153764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.136588 restraints weight = 25480.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.140996 restraints weight = 11505.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.143727 restraints weight = 6388.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4515  Z= 0.139
  Angle     :  0.495   3.890   6160  Z= 0.253
  Chirality :  0.045   0.140    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.375  26.802    725
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.58 %
    Favored  : 85.36 %
  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: -5.00 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.80 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  90 
 PHE   0.014   0.001   PHE C  86 
 TYR   0.006   0.001   TYR A  85 
 ARG   0.001   0.000   ARG A  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.623 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.8085 (tptm) cc_final: 0.7702 (mptt)
REVERT: D   38 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8164 (mmtt)
REVERT: E   86 PHE cc_start: 0.6345 (m-80) cc_final: 0.5487 (p90)
  outliers start: 10
  outliers final: 10
  residues processed: 59
  average time/residue: 0.3124
  time to fit residues: 24.3133
Evaluate side-chains
  63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   87 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  16 GLN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.152284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.135421 restraints weight = 25274.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.139683 restraints weight = 11401.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.142290 restraints weight = 6314.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4515  Z= 0.185
  Angle     :  0.526   4.333   6160  Z= 0.272
  Chirality :  0.045   0.151    700
  Planarity :  0.005   0.042    795
  Dihedral  :  5.895  32.442    725
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.99 %
    Favored  : 84.74 %
  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: -5.03 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  90 
 PHE   0.013   0.001   PHE C  86 
 TYR   0.011   0.001   TYR A  85 
 ARG   0.002   0.000   ARG D  60 

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.709 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.8107 (tptm) cc_final: 0.7729 (mptt)
REVERT: D   38 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8171 (mmtt)
REVERT: E   86 PHE cc_start: 0.6397 (m-80) cc_final: 0.5480 (p90)
  outliers start: 11
  outliers final: 11
  residues processed: 56
  average time/residue: 0.3049
  time to fit residues: 22.6036
Evaluate side-chains
  62 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue   87 CYS
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   87 CYS
Chi-restraints excluded: chain E residue   81 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0870
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 GLN ** 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 = 0.4516 r_free = 0.4516 target = 0.154124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.137457 restraints weight = 25498.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.141679 restraints weight = 11767.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.144311 restraints weight = 6582.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4515  Z= 0.143
  Angle     :  0.498   3.890   6160  Z= 0.254
  Chirality :  0.045   0.142    700
  Planarity :  0.004   0.039    795
  Dihedral  :  5.374  27.770    725
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.99 %
    Favored  : 84.74 %
  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: -4.95 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.77 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  90 
 PHE   0.012   0.001   PHE C  86 
 TYR   0.006   0.001   TYR A  85 
 ARG   0.001   0.000   ARG A  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3207.02 seconds
wall clock time: 57 minutes 29.24 seconds (3449.24 seconds total)