Starting phenix.real_space_refine
on Fri Aug 22 15:18:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx3_40825/08_2025/8sx3_40825.cif"
  }
  resolution = 4.0
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     C    3059      2.51       5
     N     816      2.21       5
     O     924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4816
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 913
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 4, 'TRANS': 112}
    Chain: "B"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1236
          Classifications: {'peptide': 154}
          Link IDs: {'PTRANS': 8, 'TRANS': 145}
    Chain: "H"
      Number of atoms: 1016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1016
          Classifications: {'peptide': 129}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 121}
    Chain: "L"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 802
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.12, per 1000 atoms: 0.23
  Number of scatterers: 4816
  At special positions: 0
  Unit cell: (55.825, 67.425, 122.525, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      17     16.00
     O     924      8.00
     N     816      7.00
     C    3059      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  21 " - pdb=" SG  CYS L  86 " 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
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN C  74 "
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 112.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      18.9% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 67
      removed outlier: 5.728A  pdb=" N   SER A  67 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 77
      No H-bonds generated for 'chain 'A' and resid 75 through 77'
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.758A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 21
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 26 through 38
    Processing helix  chain 'C' and resid 97 through 113
    Processing helix  chain 'C' and resid 114 through 122
    Processing helix  chain 'C' and resid 125 through 140
      removed outlier: 3.980A  pdb=" N   ALA C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 151
      No H-bonds generated for 'chain 'C' and resid 149 through 151'
    Processing helix  chain 'H' and resid 53 through 57
    Processing helix  chain 'H' and resid 64 through 67
    Processing helix  chain 'H' and resid 89 through 93
    Processing helix  chain 'L' and resid 25 through 28
    Processing helix  chain 'L' and resid 77 through 81
      removed outlier: 3.509A  pdb=" N   ASP L  81 " --> pdb=" O   ALA L  78 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.709A  pdb=" N   VAL A  36 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   HIS A  52 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS A  52 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE A  60 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13
      removed outlier: 3.837A  pdb=" N   LEU B  11 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA B  13 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42
      removed outlier: 7.251A  pdb=" N   GLY C  48 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   PHE C  91 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA C  50 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   LEU C  93 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 9.742A  pdb=" N   LYS C  71 " --> pdb=" O   PRO C  86 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ARG C  88 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 8.544A  pdb=" N   ARG C 154 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   VAL C  66 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ILE C  68 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   TRP H  33 " --> pdb=" O   THR H 101 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 7.044A  pdb=" N   CYS H  98 " --> pdb=" O   TRP H 121 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TRP H 121 " --> pdb=" O   CYS H  98 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ARG H 100 " --> pdb=" O   GLN H 119 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 5
    Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 12
      removed outlier: 6.296A  pdb=" N   GLN L  35 " --> pdb=" O   LEU L  44 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   LEU L  44 " --> pdb=" O   GLN L  35 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 12

    213 hydrogen bonds defined for protein.
    525 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: 0.50

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 788
        1.27 -     1.41: 1288
        1.41 -     1.55: 2767
        1.55 -     1.69: 64
        1.69 -     1.82: 26
  Bond restraints: 4933
  Sorted by residual:
  bond pdb=" CG  PRO C 141 "
       pdb=" CD  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.503  1.131  0.372 3.40e-02 8.65e+02 1.20e+02
  bond pdb=" N   PRO C 141 "
       pdb=" CD  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.473  1.554 -0.081 1.40e-02 5.10e+03 3.36e+01
  bond pdb=" CB  PRO C  82 "
       pdb=" CG  PRO C  82 "
    ideal  model  delta    sigma   weight residual
    1.492  1.658 -0.166 5.00e-02 4.00e+02 1.10e+01
  bond pdb=" CB  PRO C 141 "
       pdb=" CG  PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.492  1.593 -0.101 5.00e-02 4.00e+02 4.08e+00
  bond pdb=" CB  MET C 124 "
       pdb=" CG  MET C 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.463  0.057 3.00e-02 1.11e+03 3.60e+00
  ... (remaining 4928 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 6451
        3.46 -     6.92: 217
        6.92 -    10.38: 16
       10.38 -    13.84: 6
       13.84 -    17.30: 3
  Bond angle restraints: 6693
  Sorted by residual:
  angle pdb=" CA  PRO C 141 "
        pdb=" N   PRO C 141 "
        pdb=" CD  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     112.00   94.70   17.30 1.40e+00 5.10e-01 1.53e+02
  angle pdb=" N   PRO C 141 "
        pdb=" CD  PRO C 141 "
        pdb=" CG  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     103.20   86.58   16.62 1.50e+00 4.44e-01 1.23e+02
  angle pdb=" CA  PRO C  82 "
        pdb=" N   PRO C  82 "
        pdb=" CD  PRO C  82 "
      ideal   model   delta    sigma   weight residual
     112.00   99.04   12.96 1.40e+00 5.10e-01 8.57e+01
  angle pdb=" CA  PRO C 141 "
        pdb=" CB  PRO C 141 "
        pdb=" CG  PRO C 141 "
      ideal   model   delta    sigma   weight residual
     104.50   90.52   13.98 1.90e+00 2.77e-01 5.41e+01
  angle pdb=" CA  TYR L  47 "
        pdb=" CB  TYR L  47 "
        pdb=" CG  TYR L  47 "
      ideal   model   delta    sigma   weight residual
     113.90  122.48   -8.58 1.80e+00 3.09e-01 2.27e+01
  ... (remaining 6688 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 2625
       17.91 -    35.81: 217
       35.81 -    53.72: 61
       53.72 -    71.62: 10
       71.62 -    89.53: 3
  Dihedral angle restraints: 2916
    sinusoidal: 1176
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CA  PHE H  29 "
           pdb=" C   PHE H  29 "
           pdb=" N   ASP H  30 "
           pdb=" CA  ASP H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.42  -18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  GLU L   6 "
           pdb=" CG  GLU L   6 "
           pdb=" CD  GLU L   6 "
           pdb=" OE1 GLU L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.53  -89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASN H  79 "
           pdb=" CB  ASN H  79 "
           pdb=" CG  ASN H  79 "
           pdb=" OD1 ASN H  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.97  -67.03     2      2.00e+01 2.50e-03 1.02e+01
  ... (remaining 2913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 532
       0.069 -    0.138: 161
       0.138 -    0.207: 28
       0.207 -    0.275: 2
       0.275 -    0.344: 2
  Chirality restraints: 725
  Sorted by residual:
  chirality pdb=" CA  PRO C  82 "
            pdb=" N   PRO C  82 "
            pdb=" C   PRO C  82 "
            pdb=" CB  PRO C  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  PRO C 141 "
            pdb=" N   PRO C 141 "
            pdb=" C   PRO C 141 "
            pdb=" CB  PRO C 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CB  ILE A  71 "
            pdb=" CA  ILE A  71 "
            pdb=" CG1 ILE A  71 "
            pdb=" CG2 ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.26 2.00e-01 2.50e+01 1.69e+00
  ... (remaining 722 not shown)

  Planarity restraints: 858
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  35 "    0.042 2.00e-02 2.50e+03   3.03e-02 2.30e+01
        pdb=" CG  TRP B  35 "   -0.083 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  35 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  35 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  35 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  35 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  35 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  35 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  35 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  35 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR H 111 "   -0.081 5.00e-02 4.00e+02   1.20e-01 2.29e+01
        pdb=" N   PRO H 112 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO H 112 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO H 112 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 140 "    0.087 5.00e-02 4.00e+02   1.17e-01 2.20e+01
        pdb=" N   PRO C 141 "   -0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO C 141 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO C 141 "    0.063 5.00e-02 4.00e+02
  ... (remaining 855 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 156
        2.70 -     3.25: 4474
        3.25 -     3.80: 7562
        3.80 -     4.35: 9516
        4.35 -     4.90: 15908
  Nonbonded interactions: 37616
  Sorted by model distance:
  nonbonded pdb=" O   GLY L  75 "
            pdb=" NE2 GLN L  77 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" OD1 ASP A  91 "
            pdb=" OH  TYR A  95 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" NE2 GLN A  13 "
            pdb=" O   PRO A  14 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" NE2 GLN A  13 "
            pdb=" OE1 GLN A  16 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OH  TYR A 104 "
            pdb=" NH1 ARG C 131 "
     model   vdw
     2.264 3.120
  ... (remaining 37611 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             4.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.660
  Find NCS groups from input model:        0.010
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
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   0.372   4939  Z= 0.377
  Angle     :  1.449  17.297   6707  Z= 0.795
  Chirality :  0.066   0.344    725
  Planarity :  0.011   0.120    857
  Dihedral  : 14.594  89.530   1802
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.26 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.33), residues: 604
  helix:  0.20 (0.53), residues: 75
  sheet:  1.06 (0.34), residues: 212
  loop :  0.54 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG C 131 
 TYR   0.064   0.006   TYR L  85 
 PHE   0.063   0.007   PHE H 107 
 TRP   0.083   0.005   TRP B  35 
 HIS   0.016   0.003   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00974 ( 4933)
  covalent geometry    : angle       1.44639 ( 6693)
  SS BOND              : bond        0.01091 (    4)
  SS BOND              : angle       2.90091 (    8)
  hydrogen bonds       : bond        0.16534 (  200)
  hydrogen bonds       : angle       7.26138 (  525)
  link_BETA1-4         : bond        0.00307 (    1)
  link_BETA1-4         : angle       1.01297 (    3)
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       0.80082 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 TYR cc_start: 0.8514 (m-80) cc_final: 0.8310 (m-80)
REVERT: C   29 GLU cc_start: 0.8116 (mp0) cc_final: 0.7851 (mp0)
REVERT: H   47 TRP cc_start: 0.8838 (t60) cc_final: 0.8534 (t60)
REVERT: H   61 ASP cc_start: 0.7857 (m-30) cc_final: 0.7630 (m-30)
REVERT: L   60 PHE cc_start: 0.6118 (p90) cc_final: 0.5839 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0642
  time to fit residues: 12.4251
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.112385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.093328 restraints weight = 10229.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.096506 restraints weight = 6235.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.098823 restraints weight = 4362.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.100522 restraints weight = 3334.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.101724 restraints weight = 2713.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   4939  Z= 0.184
  Angle     :  0.767  11.721   6707  Z= 0.391
  Chirality :  0.047   0.201    725
  Planarity :  0.005   0.062    857
  Dihedral  :  5.277  34.019    712
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.96 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.33), residues: 604
  helix:  1.03 (0.60), residues: 77
  sheet:  1.11 (0.33), residues: 230
  loop :  0.19 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 131 
 TYR   0.017   0.002   TYR L  85 
 PHE   0.016   0.002   PHE H 107 
 TRP   0.040   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 4933)
  covalent geometry    : angle       0.76578 ( 6693)
  SS BOND              : bond        0.00474 (    4)
  SS BOND              : angle       1.11223 (    8)
  hydrogen bonds       : bond        0.04548 (  200)
  hydrogen bonds       : angle       6.01777 (  525)
  link_BETA1-4         : bond        0.00314 (    1)
  link_BETA1-4         : angle       1.08885 (    3)
  link_NAG-ASN         : bond        0.00239 (    1)
  link_NAG-ASN         : angle       1.43479 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.7910 (mm110) cc_final: 0.7386 (mm110)
REVERT: A  102 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: B   61 ARG cc_start: 0.7851 (ptt180) cc_final: 0.7639 (ptt180)
REVERT: B   87 TYR cc_start: 0.8395 (m-80) cc_final: 0.8176 (m-80)
REVERT: H   84 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8633 (mm-30)
REVERT: L   60 PHE cc_start: 0.6457 (p90) cc_final: 0.6244 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 140
  average time/residue: 0.0587
  time to fit residues: 10.4058
Evaluate side-chains
  118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.0010
   chunk 8 optimal weight:    0.0980
   chunk 57 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.5586

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.112047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.092867 restraints weight = 10129.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.096101 restraints weight = 6216.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098453 restraints weight = 4334.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100093 restraints weight = 3298.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.101446 restraints weight = 2697.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4939  Z= 0.144
  Angle     :  0.723  10.977   6707  Z= 0.361
  Chirality :  0.045   0.168    725
  Planarity :  0.005   0.062    857
  Dihedral  :  4.939  31.220    712
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.93 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.33), residues: 604
  helix:  0.90 (0.59), residues: 77
  sheet:  1.43 (0.33), residues: 218
  loop :  0.01 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  37 
 TYR   0.018   0.002   TYR L  85 
 PHE   0.015   0.002   PHE C  91 
 TRP   0.030   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4933)
  covalent geometry    : angle       0.72248 ( 6693)
  SS BOND              : bond        0.00427 (    4)
  SS BOND              : angle       0.96312 (    8)
  hydrogen bonds       : bond        0.04079 (  200)
  hydrogen bonds       : angle       5.58186 (  525)
  link_BETA1-4         : bond        0.00315 (    1)
  link_BETA1-4         : angle       1.27766 (    3)
  link_NAG-ASN         : bond        0.00048 (    1)
  link_NAG-ASN         : angle       1.11879 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7326 (tm-30)
REVERT: A  102 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: B   36 TYR cc_start: 0.7644 (m-80) cc_final: 0.7086 (m-80)
REVERT: B   61 ARG cc_start: 0.7876 (ptt180) cc_final: 0.7648 (ptt180)
REVERT: C   22 MET cc_start: 0.8595 (mmp) cc_final: 0.8340 (mmp)
  outliers start: 19
  outliers final: 12
  residues processed: 137
  average time/residue: 0.0520
  time to fit residues: 9.4484
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 6 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.112691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094112 restraints weight = 9935.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097246 restraints weight = 6088.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.099480 restraints weight = 4257.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.101124 restraints weight = 3256.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.102067 restraints weight = 2647.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4939  Z= 0.134
  Angle     :  0.683  10.735   6707  Z= 0.339
  Chirality :  0.044   0.168    725
  Planarity :  0.004   0.037    857
  Dihedral  :  4.785  29.219    712
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.06 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.34), residues: 604
  helix:  0.98 (0.60), residues: 77
  sheet:  1.19 (0.32), residues: 226
  loop :  0.06 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  37 
 TYR   0.018   0.002   TYR L  85 
 PHE   0.023   0.002   PHE L  60 
 TRP   0.029   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4933)
  covalent geometry    : angle       0.68134 ( 6693)
  SS BOND              : bond        0.00387 (    4)
  SS BOND              : angle       1.47556 (    8)
  hydrogen bonds       : bond        0.03781 (  200)
  hydrogen bonds       : angle       5.42627 (  525)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       1.30491 (    3)
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.01540 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8522 (p0) cc_final: 0.7722 (p0)
REVERT: A  102 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8229 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 126
  average time/residue: 0.0591
  time to fit residues: 9.7006
Evaluate side-chains
  120 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.109256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.090034 restraints weight = 10342.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.093173 restraints weight = 6372.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.095454 restraints weight = 4488.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.097147 restraints weight = 3438.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.098242 restraints weight = 2806.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4939  Z= 0.154
  Angle     :  0.683  10.531   6707  Z= 0.341
  Chirality :  0.044   0.170    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.813  27.755    712
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.32 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.34), residues: 604
  helix:  0.99 (0.62), residues: 77
  sheet:  1.18 (0.33), residues: 212
  loop :  0.03 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.020   0.002   TYR B  87 
 PHE   0.016   0.002   PHE C 117 
 TRP   0.032   0.002   TRP B  35 
 HIS   0.004   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4933)
  covalent geometry    : angle       0.68182 ( 6693)
  SS BOND              : bond        0.00369 (    4)
  SS BOND              : angle       1.02264 (    8)
  hydrogen bonds       : bond        0.03590 (  200)
  hydrogen bonds       : angle       5.23008 (  525)
  link_BETA1-4         : bond        0.00119 (    1)
  link_BETA1-4         : angle       1.16544 (    3)
  link_NAG-ASN         : bond        0.00136 (    1)
  link_NAG-ASN         : angle       0.99072 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8560 (p0) cc_final: 0.7746 (p0)
REVERT: B   36 TYR cc_start: 0.7810 (m-80) cc_final: 0.7014 (m-10)
REVERT: B   87 TYR cc_start: 0.8328 (m-80) cc_final: 0.8050 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 127
  average time/residue: 0.0571
  time to fit residues: 9.4844
Evaluate side-chains
  118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
B  30 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.102692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.082807 restraints weight = 10691.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.085812 restraints weight = 6789.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.088000 restraints weight = 4882.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089603 restraints weight = 3821.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.090789 restraints weight = 3177.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067   4939  Z= 0.281
  Angle     :  0.774  11.704   6707  Z= 0.391
  Chirality :  0.047   0.200    725
  Planarity :  0.005   0.051    857
  Dihedral  :  5.484  28.456    712
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 22.67 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.34), residues: 604
  helix:  0.55 (0.59), residues: 77
  sheet:  0.94 (0.33), residues: 225
  loop : -0.25 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 131 
 TYR   0.020   0.003   TYR A  96 
 PHE   0.024   0.004   PHE C 117 
 TRP   0.021   0.002   TRP B  35 
 HIS   0.006   0.003   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 4933)
  covalent geometry    : angle       0.77338 ( 6693)
  SS BOND              : bond        0.00178 (    4)
  SS BOND              : angle       1.00882 (    8)
  hydrogen bonds       : bond        0.04198 (  200)
  hydrogen bonds       : angle       5.46881 (  525)
  link_BETA1-4         : bond        0.00194 (    1)
  link_BETA1-4         : angle       1.25075 (    3)
  link_NAG-ASN         : bond        0.00504 (    1)
  link_NAG-ASN         : angle       1.19225 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7308 (pttm) cc_final: 0.6916 (tppt)
REVERT: A  104 TYR cc_start: 0.8454 (m-80) cc_final: 0.8112 (m-80)
REVERT: B   36 TYR cc_start: 0.8337 (m-80) cc_final: 0.7428 (m-10)
REVERT: H   30 ASP cc_start: 0.8099 (p0) cc_final: 0.7808 (p0)
REVERT: H  100 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5395 (ptm160)
  outliers start: 23
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0527
  time to fit residues: 8.7480
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   88 LEU
Chi-restraints excluded: chain H residue  100 ARG
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0670
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
C 155 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.106909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.087435 restraints weight = 10389.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.090616 restraints weight = 6473.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.092973 restraints weight = 4574.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.094668 restraints weight = 3517.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.095670 restraints weight = 2879.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4939  Z= 0.146
  Angle     :  0.725  10.302   6707  Z= 0.356
  Chirality :  0.044   0.168    725
  Planarity :  0.004   0.036    857
  Dihedral  :  5.031  25.558    712
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.16 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.34), residues: 604
  helix:  0.72 (0.61), residues: 77
  sheet:  0.92 (0.32), residues: 225
  loop : -0.22 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 100 
 TYR   0.016   0.002   TYR L  85 
 PHE   0.016   0.002   PHE A  81 
 TRP   0.023   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4933)
  covalent geometry    : angle       0.72419 ( 6693)
  SS BOND              : bond        0.00398 (    4)
  SS BOND              : angle       0.61156 (    8)
  hydrogen bonds       : bond        0.03634 (  200)
  hydrogen bonds       : angle       5.27260 (  525)
  link_BETA1-4         : bond        0.00024 (    1)
  link_BETA1-4         : angle       1.26621 (    3)
  link_NAG-ASN         : bond        0.00081 (    1)
  link_NAG-ASN         : angle       1.09723 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7280 (pttm) cc_final: 0.6890 (tppt)
REVERT: A  104 TYR cc_start: 0.8314 (m-80) cc_final: 0.8006 (m-80)
REVERT: B   36 TYR cc_start: 0.8151 (m-80) cc_final: 0.7164 (m-10)
  outliers start: 18
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0646
  time to fit residues: 10.1086
Evaluate side-chains
  114 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.106470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.086570 restraints weight = 10790.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.089769 restraints weight = 6750.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.092081 restraints weight = 4802.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.093801 restraints weight = 3730.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.094843 restraints weight = 3065.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4939  Z= 0.150
  Angle     :  0.713  10.397   6707  Z= 0.351
  Chirality :  0.044   0.167    725
  Planarity :  0.004   0.035    857
  Dihedral  :  4.945  24.349    712
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.98 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.55 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.33), residues: 604
  helix:  0.65 (0.60), residues: 77
  sheet:  0.92 (0.32), residues: 223
  loop : -0.28 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  61 
 TYR   0.020   0.002   TYR L  85 
 PHE   0.023   0.002   PHE B  83 
 TRP   0.018   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4933)
  covalent geometry    : angle       0.71295 ( 6693)
  SS BOND              : bond        0.00307 (    4)
  SS BOND              : angle       0.75164 (    8)
  hydrogen bonds       : bond        0.03793 (  200)
  hydrogen bonds       : angle       5.25218 (  525)
  link_BETA1-4         : bond        0.00160 (    1)
  link_BETA1-4         : angle       1.21526 (    3)
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       0.98537 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7254 (pttm) cc_final: 0.6831 (tppt)
REVERT: A   81 PHE cc_start: 0.8304 (m-80) cc_final: 0.7931 (m-10)
REVERT: A  104 TYR cc_start: 0.8350 (m-80) cc_final: 0.7970 (m-80)
REVERT: C   22 MET cc_start: 0.8388 (mmp) cc_final: 0.7996 (mmp)
REVERT: H   85 MET cc_start: 0.7780 (mmt) cc_final: 0.7346 (mmt)
  outliers start: 18
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0618
  time to fit residues: 9.8489
Evaluate side-chains
  119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.106596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.086410 restraints weight = 10574.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.089715 restraints weight = 6544.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.092128 restraints weight = 4641.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.093849 restraints weight = 3575.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.095141 restraints weight = 2934.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4939  Z= 0.156
  Angle     :  0.723  10.256   6707  Z= 0.356
  Chirality :  0.044   0.169    725
  Planarity :  0.003   0.033    857
  Dihedral  :  4.984  23.598    712
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.55 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.33), residues: 604
  helix:  0.61 (0.59), residues: 77
  sheet:  0.90 (0.32), residues: 217
  loop : -0.39 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  61 
 TYR   0.019   0.002   TYR L  85 
 PHE   0.019   0.002   PHE B  83 
 TRP   0.017   0.002   TRP B  35 
 HIS   0.003   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 4933)
  covalent geometry    : angle       0.72283 ( 6693)
  SS BOND              : bond        0.00264 (    4)
  SS BOND              : angle       0.75532 (    8)
  hydrogen bonds       : bond        0.03704 (  200)
  hydrogen bonds       : angle       5.18401 (  525)
  link_BETA1-4         : bond        0.00132 (    1)
  link_BETA1-4         : angle       1.18525 (    3)
  link_NAG-ASN         : bond        0.00117 (    1)
  link_NAG-ASN         : angle       0.88020 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7230 (pttm) cc_final: 0.6801 (tppt)
REVERT: A   81 PHE cc_start: 0.8251 (m-80) cc_final: 0.7896 (m-10)
REVERT: A  104 TYR cc_start: 0.8294 (m-80) cc_final: 0.7956 (m-80)
REVERT: C   22 MET cc_start: 0.8417 (mmp) cc_final: 0.8053 (mmp)
REVERT: H   85 MET cc_start: 0.7505 (mmt) cc_final: 0.7294 (mmt)
  outliers start: 17
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0644
  time to fit residues: 9.8139
Evaluate side-chains
  118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0470
   chunk 28 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.087378 restraints weight = 10517.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.090574 restraints weight = 6561.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.092989 restraints weight = 4709.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.094742 restraints weight = 3620.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.095901 restraints weight = 2953.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4939  Z= 0.151
  Angle     :  0.729  10.316   6707  Z= 0.362
  Chirality :  0.044   0.165    725
  Planarity :  0.003   0.026    857
  Dihedral  :  4.955  23.184    712
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.36 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.33), residues: 604
  helix:  0.55 (0.59), residues: 77
  sheet:  0.86 (0.32), residues: 217
  loop : -0.44 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  61 
 TYR   0.019   0.002   TYR L  85 
 PHE   0.015   0.002   PHE H 107 
 TRP   0.017   0.002   TRP B  35 
 HIS   0.003   0.001   HIS L  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4933)
  covalent geometry    : angle       0.72817 ( 6693)
  SS BOND              : bond        0.00283 (    4)
  SS BOND              : angle       0.78767 (    8)
  hydrogen bonds       : bond        0.03688 (  200)
  hydrogen bonds       : angle       5.13282 (  525)
  link_BETA1-4         : bond        0.00304 (    1)
  link_BETA1-4         : angle       1.24036 (    3)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       0.83045 (    3)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7214 (pttm) cc_final: 0.6765 (tppt)
REVERT: A   81 PHE cc_start: 0.8266 (m-80) cc_final: 0.7866 (m-10)
REVERT: A  104 TYR cc_start: 0.8254 (m-80) cc_final: 0.7919 (m-80)
REVERT: C   22 MET cc_start: 0.8421 (mmp) cc_final: 0.8080 (mmp)
  outliers start: 19
  outliers final: 17
  residues processed: 121
  average time/residue: 0.0613
  time to fit residues: 9.6008
Evaluate side-chains
  121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   58 TYR
Chi-restraints excluded: chain C residue   76 SER
Chi-restraints excluded: chain C residue   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   44 LEU
Chi-restraints excluded: chain L residue   45 LEU
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  108 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.0970
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
B  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.102826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.082272 restraints weight = 10952.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.085343 restraints weight = 7057.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.087645 restraints weight = 5132.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.089308 restraints weight = 4030.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090336 restraints weight = 3342.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   4939  Z= 0.225
  Angle     :  0.768  10.400   6707  Z= 0.387
  Chirality :  0.045   0.174    725
  Planarity :  0.004   0.031    857
  Dihedral  :  5.293  25.321    712
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.78 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.34), residues: 604
  helix:  0.58 (0.58), residues: 77
  sheet:  0.72 (0.33), residues: 221
  loop : -0.52 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  61 
 TYR   0.021   0.002   TYR L  85 
 PHE   0.022   0.003   PHE B  83 
 TRP   0.014   0.002   TRP B  35 
 HIS   0.005   0.002   HIS A  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 4933)
  covalent geometry    : angle       0.76746 ( 6693)
  SS BOND              : bond        0.00225 (    4)
  SS BOND              : angle       0.85957 (    8)
  hydrogen bonds       : bond        0.03930 (  200)
  hydrogen bonds       : angle       5.27820 (  525)
  link_BETA1-4         : bond        0.00064 (    1)
  link_BETA1-4         : angle       1.03550 (    3)
  link_NAG-ASN         : bond        0.00410 (    1)
  link_NAG-ASN         : angle       0.97577 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 866.30 seconds
wall clock time: 15 minutes 39.88 seconds (939.88 seconds total)