Starting phenix.real_space_refine
on Thu Mar 13 04:05:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fab_50271/03_2025/9fab_50271_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fab_50271/03_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_50271/03_2025/9fab_50271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fab_50271/03_2025/9fab_50271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fab_50271/03_2025/9fab_50271_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fab_50271/03_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-5624/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: 3.79, per 1000 atoms: 0.44
  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=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  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: 1.95
  Conformation dependent library (CDL) restraints added in 745.4 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: 0.81
  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: 2.63

  Time building geometry restraints manager: 2.43 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: 3767
       14.68 -    29.37: 309
       29.37 -    44.05: 94
       44.05 -    58.73: 95
       58.73 -    73.42: 30
  Dihedral angle restraints: 4295
    sinusoidal: 2375
      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 4292 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: 3585
        2.38 -     2.93: 18474
        2.93 -     3.49: 19243
        3.49 -     4.04: 28985
        4.04 -     4.60: 40178
  Nonbonded interactions: 110465
  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 110460 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:             1.860
  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:             0.150
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.590
  Find NCS groups from input model:        0.120
  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:2.940
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.150
-------------------------------------------------------------------------------
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= 0.691
  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 : 2.531

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  : 0.720 
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: 0.3143
  time to fit residues: 54.7029
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  : 0.671 
-------------------------------------------------------------------------------
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:    1.9990
   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:    1.2784

-------------------------------------------------------------------------------
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 = 0.4461 r_free = 0.4461 target = 0.152526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.135957 restraints weight = 25735.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.140189 restraints weight = 11449.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.142721 restraints weight = 6288.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4515  Z= 0.258
  Angle     :  0.699   4.583   6160  Z= 0.380
  Chirality :  0.049   0.237    700
  Planarity :  0.005   0.039    795
  Dihedral  :  5.919  17.703    725
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  :  8.04 %
    Favored  : 89.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.65 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E  34 
 PHE   0.016   0.001   PHE C   2 
 TYR   0.028   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
  97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7889 (tptm) cc_final: 0.7611 (mptt)
REVERT: C  110 LYS cc_start: 0.8011 (tptm) cc_final: 0.7558 (mptt)
REVERT: D   38 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8032 (mmtt)
REVERT: E   84 ASP cc_start: 0.5857 (m-30) cc_final: 0.5619 (m-30)
REVERT: E   86 PHE cc_start: 0.6708 (m-80) cc_final: 0.5875 (p90)
  outliers start: 13
  outliers final: 6
  residues processed: 94
  average time/residue: 0.2840
  time to fit residues: 35.2353
Evaluate side-chains
  64 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain D residue   96 VAL
Chi-restraints excluded: chain E residue   96 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 42 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.9584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.153695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.136748 restraints weight = 25570.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.141136 restraints weight = 11554.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.143703 restraints weight = 6329.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.4375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4515  Z= 0.205
  Angle     :  0.591   4.324   6160  Z= 0.315
  Chirality :  0.047   0.191    700
  Planarity :  0.005   0.039    795
  Dihedral  :  5.479  21.611    725
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.55 %
    Favored  : 87.22 %
  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: -4.72 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.16), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  34 
 PHE   0.011   0.001   PHE A   2 
 TYR   0.013   0.002   TYR A  31 
 ARG   0.002   0.000   ARG A  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
  86 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7858 (tptm) cc_final: 0.7555 (mptt)
REVERT: C   87 CYS cc_start: 0.5010 (m) cc_final: 0.4731 (m)
REVERT: C   88 GLN cc_start: 0.7327 (tm-30) cc_final: 0.6991 (tm-30)
REVERT: C  110 LYS cc_start: 0.7921 (tptm) cc_final: 0.7564 (mptt)
REVERT: D   38 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8001 (mmtt)
REVERT: E   84 ASP cc_start: 0.5881 (m-30) cc_final: 0.5545 (m-30)
REVERT: E   86 PHE cc_start: 0.6292 (m-80) cc_final: 0.5879 (p90)
REVERT: E   88 GLN cc_start: 0.6450 (tm-30) cc_final: 0.6229 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 82
  average time/residue: 0.2687
  time to fit residues: 29.2846
Evaluate side-chains
  70 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain C residue   51 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
D  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.150735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.134409 restraints weight = 26128.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.138511 restraints weight = 11721.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.140993 restraints weight = 6429.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.4226

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= 0.244
  Angle     :  0.595   4.076   6160  Z= 0.318
  Chirality :  0.048   0.203    700
  Planarity :  0.005   0.040    795
  Dihedral  :  6.273  31.714    725
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 11.34 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.92 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  90 
 PHE   0.010   0.002   PHE B  61 
 TYR   0.014   0.002   TYR A  85 
 ARG   0.002   0.000   ARG D  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
  85 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.7940 (tptm) cc_final: 0.7508 (mptt)
REVERT: D   38 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8023 (mmtt)
REVERT: E   86 PHE cc_start: 0.6322 (m-80) cc_final: 0.5721 (p90)
  outliers start: 14
  outliers final: 11
  residues processed: 77
  average time/residue: 0.2967
  time to fit residues: 29.7034
Evaluate side-chains
  70 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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   38 LYS
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   68 ASN
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   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.9788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.149322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.132981 restraints weight = 25509.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.137087 restraints weight = 11188.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.139543 restraints weight = 6027.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4515  Z= 0.292
  Angle     :  0.630   4.291   6160  Z= 0.337
  Chirality :  0.048   0.202    700
  Planarity :  0.005   0.046    795
  Dihedral  :  7.177  41.514    725
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 11.55 %
    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: -5.15 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D  90 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.016   0.002   TYR C  85 
 ARG   0.003   0.001   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
  76 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8075 (tptm) cc_final: 0.7639 (mptt)
REVERT: D   38 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8148 (mmtt)
REVERT: E   86 PHE cc_start: 0.6212 (m-80) cc_final: 0.5640 (p90)
  outliers start: 15
  outliers final: 13
  residues processed: 69
  average time/residue: 0.3053
  time to fit residues: 27.3385
Evaluate side-chains
  66 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
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   51 SER
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   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   68 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4472 r_free = 0.4472 target = 0.151297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.134908 restraints weight = 25411.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.139123 restraints weight = 11203.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.141671 restraints weight = 6047.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.5007

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= 0.180
  Angle     :  0.540   3.933   6160  Z= 0.283
  Chirality :  0.047   0.170    700
  Planarity :  0.005   0.043    795
  Dihedral  :  6.085  30.209    725
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.58 %
    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: -5.04 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (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 D  61 
 TYR   0.011   0.001   TYR C  85 
 ARG   0.002   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
  76 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8061 (tptm) cc_final: 0.7682 (mptt)
REVERT: D   38 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8130 (mmtt)
REVERT: E   84 ASP cc_start: 0.6024 (m-30) cc_final: 0.5741 (m-30)
REVERT: E   86 PHE cc_start: 0.6106 (m-80) cc_final: 0.5652 (p90)
  outliers start: 11
  outliers final: 10
  residues processed: 68
  average time/residue: 0.3070
  time to fit residues: 27.1858
Evaluate side-chains
  69 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 PHE
Chi-restraints excluded: chain A residue   51 SER
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   51 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0020
   chunk 6 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6390

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.152455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.136049 restraints weight = 25547.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.140373 restraints weight = 11120.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.142893 restraints weight = 5942.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.5198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4515  Z= 0.161
  Angle     :  0.516   4.707   6160  Z= 0.267
  Chirality :  0.046   0.157    700
  Planarity :  0.005   0.041    795
  Dihedral  :  5.607  26.974    725
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.99 %
    Favored  : 84.95 %
  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: -4.96 (0.23), 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   0.010   0.001   TRP A  90 
 PHE   0.006   0.001   PHE C  86 
 TYR   0.009   0.001   TYR A  85 
 ARG   0.001   0.000   ARG A  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
  82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8047 (tptm) cc_final: 0.7681 (mptt)
REVERT: D   38 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8011 (mmtt)
REVERT: E   84 ASP cc_start: 0.5956 (m-30) cc_final: 0.5754 (m-30)
REVERT: E   86 PHE cc_start: 0.6147 (m-80) cc_final: 0.5717 (p90)
  outliers start: 10
  outliers final: 9
  residues processed: 74
  average time/residue: 0.2984
  time to fit residues: 28.7438
Evaluate side-chains
  71 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
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   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain E residue   81 ASP
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:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.150950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.135187 restraints weight = 25911.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.139276 restraints weight = 11438.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.141664 restraints weight = 6183.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4515  Z= 0.217
  Angle     :  0.546   3.985   6160  Z= 0.287
  Chirality :  0.046   0.172    700
  Planarity :  0.005   0.043    795
  Dihedral  :  6.280  34.269    725
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 12.37 %
    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: -5.04 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  90 
 PHE   0.006   0.001   PHE B  86 
 TYR   0.013   0.002   TYR C  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
  74 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8122 (tptm) cc_final: 0.7770 (mptt)
REVERT: D   38 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8045 (mmtt)
REVERT: D   90 TRP cc_start: 0.7266 (m-10) cc_final: 0.7033 (m-10)
REVERT: E   86 PHE cc_start: 0.6231 (m-80) cc_final: 0.5737 (p90)
  outliers start: 14
  outliers final: 11
  residues processed: 66
  average time/residue: 0.2683
  time to fit residues: 23.8909
Evaluate side-chains
  68 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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 E residue   81 ASP
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:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.152158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.135786 restraints weight = 25597.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.140134 restraints weight = 11126.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.142654 restraints weight = 5963.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.5491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4515  Z= 0.188
  Angle     :  0.532   3.939   6160  Z= 0.278
  Chirality :  0.046   0.179    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.061  31.997    725
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.16 %
    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: -5.06 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  90 
 PHE   0.007   0.001   PHE E  86 
 TYR   0.010   0.001   TYR C  85 
 ARG   0.001   0.000   ARG D  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
  74 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8062 (tp)
REVERT: C  110 LYS cc_start: 0.8098 (tptm) cc_final: 0.7703 (mptt)
REVERT: D   38 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8087 (mmtt)
REVERT: D   90 TRP cc_start: 0.7251 (m-10) cc_final: 0.7044 (m-10)
REVERT: E   21 THR cc_start: 0.7981 (m) cc_final: 0.7767 (p)
REVERT: E   86 PHE cc_start: 0.6174 (m-80) cc_final: 0.5825 (p90)
  outliers start: 13
  outliers final: 11
  residues processed: 66
  average time/residue: 0.2962
  time to fit residues: 26.1178
Evaluate side-chains
  70 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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   72 LEU
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 E residue   81 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 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:
** B  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 = 0.4495 r_free = 0.4495 target = 0.153736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.137451 restraints weight = 25215.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.141738 restraints weight = 11064.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.144307 restraints weight = 5946.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.5604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4515  Z= 0.179
  Angle     :  0.520   3.913   6160  Z= 0.270
  Chirality :  0.046   0.174    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.746  29.249    725
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.58 %
    Favored  : 84.95 %
  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: -5.00 (0.24), 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   0.009   0.001   TRP B  90 
 PHE   0.006   0.001   PHE E  86 
 TYR   0.008   0.001   TYR C  85 
 ARG   0.001   0.000   ARG A  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
  74 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8084 (tptm) cc_final: 0.7743 (mptt)
REVERT: D   38 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8053 (mmtt)
REVERT: D   90 TRP cc_start: 0.7278 (m-10) cc_final: 0.7004 (m-10)
REVERT: E   84 ASP cc_start: 0.5917 (m-30) cc_final: 0.5677 (m-30)
  outliers start: 12
  outliers final: 11
  residues processed: 66
  average time/residue: 0.2908
  time to fit residues: 25.4909
Evaluate side-chains
  70 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
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 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:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.153834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.138309 restraints weight = 25602.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.142325 restraints weight = 11429.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.144679 restraints weight = 6222.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.5784

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= 0.207
  Angle     :  0.543   4.125   6160  Z= 0.286
  Chirality :  0.046   0.167    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.109  33.011    725
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.99 %
    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 (0.24), 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   0.010   0.001   TRP B  90 
 PHE   0.026   0.001   PHE E  86 
 TYR   0.010   0.001   TYR C  85 
 ARG   0.002   0.000   ARG D  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3405.67 seconds
wall clock time: 58 minutes 53.38 seconds (3533.38 seconds total)