Starting phenix.real_space_refine
on Wed Sep 17 12:12:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fab_50271/09_2025/9fab_50271_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fab_50271/09_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_50271/09_2025/9fab_50271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fab_50271/09_2025/9fab_50271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fab_50271/09_2025/9fab_50271_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fab_50271/09_2025/9fab_50271_trim.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 1.70, per 1000 atoms: 0.20
  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 B  22 " - pdb=" SG  CYS B  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  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: 0.76
  Conformation dependent library (CDL) restraints added in 302.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.29
  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: 1.85

  Time building geometry restraints manager: 1.09 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             3.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.030
-------------------------------------------------------------------------------
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   4525  Z= 0.472
  Angle     :  1.598   9.728   6185  Z= 0.931
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.005   0.002   ARG E  60 
 TYR   0.040   0.008   TYR B  85 
 PHE   0.022   0.005   PHE A   2 
 TRP   0.028   0.009   TRP A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.01018 ( 4515)
  covalent geometry    : angle       1.56559 ( 6160)
  SS BOND              : bond        0.01215 (    5)
  SS BOND              : angle       5.96825 (   10)
  hydrogen bonds       : bond        0.20028 (   82)
  hydrogen bonds       : angle       7.89005 (  243)
  link_NAG-ASN         : bond        0.00419 (    5)
  link_NAG-ASN         : angle       4.75514 (   15)

*********************** 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  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ILE cc_start: 0.8487 (mt) cc_final: 0.8167 (mt)
REVERT: A   78 GLN cc_start: 0.7987 (tt0) cc_final: 0.7780 (tt0)
REVERT: A  110 LYS cc_start: 0.7916 (tptm) cc_final: 0.7644 (mptt)
REVERT: A  115 VAL cc_start: 0.6206 (t) cc_final: 0.5969 (t)
REVERT: C   88 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7251 (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: 0.8285 (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: 0.6937 (pm20)
REVERT: E   61 PHE cc_start: 0.5374 (p90) cc_final: 0.5049 (t80)
REVERT: E   72 LEU cc_start: 0.8601 (tp) cc_final: 0.8393 (pp)
REVERT: E   86 PHE cc_start: 0.6696 (m-80) cc_final: 0.6021 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1509
  time to fit residues: 26.5584
Evaluate side-chains
  65 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.153654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.137124 restraints weight = 25639.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.141300 restraints weight = 11390.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.143814 restraints weight = 6298.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.145394 restraints weight = 4018.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.146530 restraints weight = 2876.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4525  Z= 0.164
  Angle     :  0.686   4.747   6185  Z= 0.370
  Chirality :  0.049   0.223    700
  Planarity :  0.005   0.037    795
  Dihedral  :  5.488  16.862    725
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  8.45 %
    Favored  : 89.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.56 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.47 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  60 
 TYR   0.026   0.002   TYR A  31 
 PHE   0.016   0.001   PHE C   2 
 TRP   0.013   0.001   TRP E  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4515)
  covalent geometry    : angle       0.67524 ( 6160)
  SS BOND              : bond        0.00485 (    5)
  SS BOND              : angle       2.58746 (   10)
  hydrogen bonds       : bond        0.03722 (   82)
  hydrogen bonds       : angle       5.59158 (  243)
  link_NAG-ASN         : bond        0.00075 (    5)
  link_NAG-ASN         : angle       1.52092 (   15)

*********************** 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: 10
    poor density    : 84
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8715 (mtpp)
REVERT: A  110 LYS cc_start: 0.7873 (tptm) cc_final: 0.7628 (mptt)
REVERT: C  110 LYS cc_start: 0.8043 (tptm) cc_final: 0.7530 (mptt)
REVERT: D   38 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7979 (mmtt)
REVERT: E   57 ILE cc_start: 0.8508 (mt) cc_final: 0.8306 (mt)
REVERT: E   86 PHE cc_start: 0.6616 (m-80) cc_final: 0.6021 (p90)
  outliers start: 10
  outliers final: 4
  residues processed: 90
  average time/residue: 0.1283
  time to fit residues: 15.4665
Evaluate side-chains
  67 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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   68 ASN
Chi-restraints excluded: chain D residue   96 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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
B  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.149667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.133660 restraints weight = 26132.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.137717 restraints weight = 11806.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.140132 restraints weight = 6470.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.141619 restraints weight = 4120.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.142617 restraints weight = 2961.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4525  Z= 0.224
  Angle     :  0.735   5.437   6185  Z= 0.393
  Chirality :  0.049   0.227    700
  Planarity :  0.006   0.054    795
  Dihedral  :  6.992  35.464    725
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.93 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.98 (0.21), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.79 (0.16), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  60 
 TYR   0.020   0.003   TYR C  85 
 PHE   0.014   0.002   PHE A   2 
 TRP   0.007   0.002   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 4515)
  covalent geometry    : angle       0.71222 ( 6160)
  SS BOND              : bond        0.00775 (    5)
  SS BOND              : angle       3.48187 (   10)
  hydrogen bonds       : bond        0.03940 (   82)
  hydrogen bonds       : angle       5.12593 (  243)
  link_NAG-ASN         : bond        0.00465 (    5)
  link_NAG-ASN         : angle       2.51932 (   15)

*********************** 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
  73 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8030 (tptm) cc_final: 0.7674 (mptt)
REVERT: D   38 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8255 (mmtt)
REVERT: E   86 PHE cc_start: 0.6630 (m-80) cc_final: 0.5920 (p90)
  outliers start: 11
  outliers final: 7
  residues processed: 71
  average time/residue: 0.1477
  time to fit residues: 13.6033
Evaluate side-chains
  59 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
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   51 SER
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   96 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.151981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.135650 restraints weight = 25913.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.139817 restraints weight = 11531.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.142376 restraints weight = 6274.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.143900 restraints weight = 3964.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.144853 restraints weight = 2834.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4525  Z= 0.117
  Angle     :  0.576   4.787   6185  Z= 0.302
  Chirality :  0.047   0.182    700
  Planarity :  0.005   0.042    795
  Dihedral  :  6.100  30.100    725
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.16 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.95 (0.21), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.77 (0.16), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  60 
 TYR   0.012   0.001   TYR A  85 
 PHE   0.010   0.001   PHE C   2 
 TRP   0.005   0.001   TRP A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4515)
  covalent geometry    : angle       0.56835 ( 6160)
  SS BOND              : bond        0.00658 (    5)
  SS BOND              : angle       2.03782 (   10)
  hydrogen bonds       : bond        0.02833 (   82)
  hydrogen bonds       : angle       4.85854 (  243)
  link_NAG-ASN         : bond        0.00072 (    5)
  link_NAG-ASN         : angle       1.16621 (   15)

*********************** 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
  81 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (mttm)
REVERT: C  110 LYS cc_start: 0.8035 (tptm) cc_final: 0.7548 (mptt)
REVERT: D   38 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8059 (mmtt)
REVERT: E   86 PHE cc_start: 0.6422 (m-80) cc_final: 0.5919 (p90)
  outliers start: 11
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1355
  time to fit residues: 13.5254
Evaluate side-chains
  67 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain C residue   12 VAL
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0470
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  78 GLN
** D  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.151762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.135874 restraints weight = 25871.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.139902 restraints weight = 11570.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.142276 restraints weight = 6341.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.143736 restraints weight = 4073.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.144789 restraints weight = 2954.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6871
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4525  Z= 0.117
  Angle     :  0.565   4.571   6185  Z= 0.296
  Chirality :  0.047   0.182    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.992  29.644    725
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.94 (0.22), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.76 (0.17), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.011   0.001   TYR C  85 
 PHE   0.008   0.001   PHE A   2 
 TRP   0.005   0.001   TRP A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4515)
  covalent geometry    : angle       0.54755 ( 6160)
  SS BOND              : bond        0.00846 (    5)
  SS BOND              : angle       3.33050 (   10)
  hydrogen bonds       : bond        0.02562 (   82)
  hydrogen bonds       : angle       4.63249 (  243)
  link_NAG-ASN         : bond        0.00085 (    5)
  link_NAG-ASN         : angle       1.08383 (   15)

*********************** 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
  78 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   84 ASP cc_start: 0.7202 (m-30) cc_final: 0.6995 (m-30)
REVERT: C  110 LYS cc_start: 0.8063 (tptm) cc_final: 0.7684 (mptt)
REVERT: D   38 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8067 (mmtt)
REVERT: E   86 PHE cc_start: 0.6501 (m-80) cc_final: 0.5803 (p90)
  outliers start: 13
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1388
  time to fit residues: 12.7888
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  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
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   68 ASN
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain C residue   12 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.152776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.136861 restraints weight = 25644.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.140814 restraints weight = 11437.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.143178 restraints weight = 6314.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.144645 restraints weight = 4031.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.145392 restraints weight = 2918.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.4396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4525  Z= 0.110
  Angle     :  0.542   4.517   6185  Z= 0.282
  Chirality :  0.046   0.174    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.859  29.021    725
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.90 (0.23), 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
 ARG   0.001   0.000   ARG A  60 
 TYR   0.013   0.001   TYR C  85 
 PHE   0.008   0.001   PHE E  86 
 TRP   0.006   0.001   TRP A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4515)
  covalent geometry    : angle       0.52998 ( 6160)
  SS BOND              : bond        0.00706 (    5)
  SS BOND              : angle       2.68085 (   10)
  hydrogen bonds       : bond        0.02382 (   82)
  hydrogen bonds       : angle       4.52701 (  243)
  link_NAG-ASN         : bond        0.00090 (    5)
  link_NAG-ASN         : angle       1.03343 (   15)

*********************** 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
  82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7373 (tm-30)
REVERT: C  110 LYS cc_start: 0.8046 (tptm) cc_final: 0.7666 (mptt)
REVERT: D   38 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8079 (mmtt)
REVERT: E   86 PHE cc_start: 0.6108 (m-80) cc_final: 0.5737 (p90)
  outliers start: 13
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1456
  time to fit residues: 14.1357
Evaluate side-chains
  68 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
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   51 SER
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain D residue   61 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6758

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.153479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.137156 restraints weight = 25767.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.141372 restraints weight = 11350.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.143829 restraints weight = 6136.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.145332 restraints weight = 3895.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.146363 restraints weight = 2813.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6853
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4525  Z= 0.099
  Angle     :  0.531   4.658   6185  Z= 0.275
  Chirality :  0.046   0.165    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.612  26.898    725
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.87 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.70 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.009   0.001   TYR C  85 
 PHE   0.008   0.001   PHE E  86 
 TRP   0.022   0.001   TRP C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4515)
  covalent geometry    : angle       0.51842 ( 6160)
  SS BOND              : bond        0.00629 (    5)
  SS BOND              : angle       2.79361 (   10)
  hydrogen bonds       : bond        0.02143 (   82)
  hydrogen bonds       : angle       4.37988 (  243)
  link_NAG-ASN         : bond        0.00138 (    5)
  link_NAG-ASN         : angle       0.92173 (   15)

*********************** 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
  81 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8058 (tptm) cc_final: 0.7717 (mptt)
REVERT: D   38 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8053 (mmtt)
REVERT: E   86 PHE cc_start: 0.6166 (m-80) cc_final: 0.5777 (p90)
  outliers start: 10
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1445
  time to fit residues: 13.9497
Evaluate side-chains
  73 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4484 r_free = 0.4484 target = 0.153222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.137251 restraints weight = 25356.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.141326 restraints weight = 11386.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.143686 restraints weight = 6220.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.145242 restraints weight = 3983.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.146226 restraints weight = 2844.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.4410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4525  Z= 0.106
  Angle     :  0.535   6.608   6185  Z= 0.277
  Chirality :  0.046   0.166    700
  Planarity :  0.005   0.041    795
  Dihedral  :  5.737  28.550    725
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.84 (0.23), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.68 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  60 
 TYR   0.010   0.001   TYR C  85 
 PHE   0.007   0.001   PHE E  86 
 TRP   0.031   0.002   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4515)
  covalent geometry    : angle       0.52182 ( 6160)
  SS BOND              : bond        0.00675 (    5)
  SS BOND              : angle       2.83276 (   10)
  hydrogen bonds       : bond        0.02284 (   82)
  hydrogen bonds       : angle       4.45498 (  243)
  link_NAG-ASN         : bond        0.00092 (    5)
  link_NAG-ASN         : angle       1.00465 (   15)

*********************** 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
  82 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8060 (tptm) cc_final: 0.7720 (mptt)
REVERT: D   38 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8073 (mmtt)
REVERT: D   90 TRP cc_start: 0.7184 (m-10) cc_final: 0.6937 (m-10)
REVERT: E   86 PHE cc_start: 0.6119 (m-80) cc_final: 0.5906 (p90)
  outliers start: 12
  outliers final: 12
  residues processed: 74
  average time/residue: 0.1425
  time to fit residues: 13.8938
Evaluate side-chains
  76 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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   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   68 ASN
Chi-restraints excluded: chain D residue   51 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.153003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.137317 restraints weight = 25501.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.141331 restraints weight = 11454.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.143721 restraints weight = 6286.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.145173 restraints weight = 3998.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.146126 restraints weight = 2889.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4525  Z= 0.104
  Angle     :  0.528   4.681   6185  Z= 0.274
  Chirality :  0.046   0.161    700
  Planarity :  0.005   0.041    795
  Dihedral  :  5.751  29.626    725
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.85 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.69 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  60 
 TYR   0.009   0.001   TYR C  85 
 PHE   0.007   0.001   PHE E  86 
 TRP   0.046   0.003   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4515)
  covalent geometry    : angle       0.52060 ( 6160)
  SS BOND              : bond        0.00656 (    5)
  SS BOND              : angle       2.07909 (   10)
  hydrogen bonds       : bond        0.02411 (   82)
  hydrogen bonds       : angle       4.32696 (  243)
  link_NAG-ASN         : bond        0.00076 (    5)
  link_NAG-ASN         : angle       0.99364 (   15)

*********************** 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
  79 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8079 (tptm) cc_final: 0.7734 (mptt)
REVERT: D   38 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8005 (mmtt)
REVERT: E   86 PHE cc_start: 0.6167 (m-80) cc_final: 0.5871 (p90)
  outliers start: 12
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1398
  time to fit residues: 13.1660
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  : 0.244 
-------------------------------------------------------------------------------
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   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   68 ASN
Chi-restraints excluded: chain D residue   51 SER
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 44 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4502 r_free = 0.4502 target = 0.154545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.138481 restraints weight = 25393.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.142675 restraints weight = 11346.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.145147 restraints weight = 6171.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.146696 restraints weight = 3898.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.147703 restraints weight = 2774.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.5373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4525  Z= 0.102
  Angle     :  0.530   6.252   6185  Z= 0.272
  Chirality :  0.046   0.175    700
  Planarity :  0.005   0.040    795
  Dihedral  :  5.666  28.614    725
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.80 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.010   0.001   TYR C  85 
 PHE   0.006   0.001   PHE E  86 
 TRP   0.037   0.002   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4515)
  covalent geometry    : angle       0.51867 ( 6160)
  SS BOND              : bond        0.00637 (    5)
  SS BOND              : angle       2.60128 (   10)
  hydrogen bonds       : bond        0.02350 (   82)
  hydrogen bonds       : angle       4.32366 (  243)
  link_NAG-ASN         : bond        0.00148 (    5)
  link_NAG-ASN         : angle       0.97166 (   15)

********************** 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
  77 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  110 LYS cc_start: 0.8113 (tptm) cc_final: 0.7793 (mptt)
REVERT: D   38 LYS cc_start: 0.8496 (mtmt) cc_final: 0.7990 (mmtt)
REVERT: E   21 THR cc_start: 0.7920 (m) cc_final: 0.7678 (p)
  outliers start: 12
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1439
  time to fit residues: 13.0297
Evaluate side-chains
  75 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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   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   68 ASN
Chi-restraints excluded: chain D residue   51 SER
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 7 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.155366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.139697 restraints weight = 25443.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.143658 restraints weight = 11484.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.146014 restraints weight = 6315.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.147505 restraints weight = 4064.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.148506 restraints weight = 2935.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4525  Z= 0.105
  Angle     :  0.531   5.966   6185  Z= 0.273
  Chirality :  0.046   0.160    700
  Planarity :  0.005   0.037    795
  Dihedral  :  5.672  28.767    725
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.20 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.81 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  60 
 TYR   0.009   0.001   TYR C  85 
 PHE   0.022   0.001   PHE E  86 
 TRP   0.033   0.002   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4515)
  covalent geometry    : angle       0.51956 ( 6160)
  SS BOND              : bond        0.00672 (    5)
  SS BOND              : angle       2.55800 (   10)
  hydrogen bonds       : bond        0.02250 (   82)
  hydrogen bonds       : angle       4.27449 (  243)
  link_NAG-ASN         : bond        0.00132 (    5)
  link_NAG-ASN         : angle       0.98786 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.93 seconds
wall clock time: 34 minutes 37.84 seconds (2077.84 seconds total)