Starting phenix.real_space_refine
on Sat May 10 03:14:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sx3_40825/05_2025/8sx3_40825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sx3_40825/05_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_40825/05_2025/8sx3_40825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sx3_40825/05_2025/8sx3_40825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sx3_40825/05_2025/8sx3_40825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sx3_40825/05_2025/8sx3_40825.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.13, per 1000 atoms: 0.86
  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: 1.29
  Conformation dependent library (CDL) restraints added in 632.4 milliseconds
  

  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: 0.65
  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: 1.27

  Time building geometry restraints manager: 1.49 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:             3.750
  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:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     16.650
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.650
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.083   0.005   TRP B  35 
 HIS   0.016   0.003   HIS L  29 
 PHE   0.063   0.007   PHE H 107 
 TYR   0.064   0.006   TYR L  85 
 ARG   0.018   0.002   ARG C 131 

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

*********************** 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  : 0.605 
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: 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: 0.1857
  time to fit residues: 35.2553
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  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN
A  16 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.111874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092768 restraints weight = 10170.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.095897 restraints weight = 6257.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098195 restraints weight = 4396.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4939  Z= 0.187
  Angle     :  0.767  11.645   6707  Z= 0.391
  Chirality :  0.047   0.198    725
  Planarity :  0.005   0.063    857
  Dihedral  :  5.283  34.174    712
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.33), residues: 604
  helix:  1.03 (0.60), residues: 77
  sheet:  1.23 (0.33), residues: 221
  loop :  0.13 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP B  35 
 HIS   0.006   0.001   HIS L  29 
 PHE   0.016   0.002   PHE H 107 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.006   0.001   ARG C 131 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    1)
  link_NAG-ASN         : angle       1.43904 (    3)
  link_BETA1-4         : bond        0.00059 (    1)
  link_BETA1-4         : angle       1.13037 (    3)
  hydrogen bonds       : bond        0.04551 (  200)
  hydrogen bonds       : angle       5.99054 (  525)
  SS BOND              : bond        0.00402 (    4)
  SS BOND              : angle       1.09738 (    8)
  covalent geometry    : bond        0.00448 ( 4933)
  covalent geometry    : angle       0.76567 ( 6693)

*********************** 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
  149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A   16 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7157 (mm-40)
REVERT: A  102 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: B   61 ARG cc_start: 0.7952 (ptt180) cc_final: 0.7685 (ptt180)
REVERT: B   83 PHE cc_start: 0.7666 (m-80) cc_final: 0.7454 (m-80)
REVERT: B   87 TYR cc_start: 0.8414 (m-80) cc_final: 0.8174 (m-80)
REVERT: L   60 PHE cc_start: 0.6569 (p90) cc_final: 0.6335 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1733
  time to fit residues: 31.1013
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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 29 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0030
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6990

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.110607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.091229 restraints weight = 10159.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.094393 restraints weight = 6299.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.096535 restraints weight = 4438.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4939  Z= 0.154
  Angle     :  0.726  10.997   6707  Z= 0.363
  Chirality :  0.045   0.178    725
  Planarity :  0.005   0.062    857
  Dihedral  :  4.980  31.423    712
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.51 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.33), residues: 604
  helix:  0.63 (0.58), residues: 77
  sheet:  1.37 (0.34), residues: 209
  loop :  0.11 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  35 
 HIS   0.005   0.001   HIS L  29 
 PHE   0.016   0.002   PHE C  91 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.014   0.001   ARG C  37 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    1)
  link_NAG-ASN         : angle       1.13116 (    3)
  link_BETA1-4         : bond        0.00262 (    1)
  link_BETA1-4         : angle       1.25612 (    3)
  hydrogen bonds       : bond        0.04090 (  200)
  hydrogen bonds       : angle       5.63319 (  525)
  SS BOND              : bond        0.00393 (    4)
  SS BOND              : angle       1.00474 (    8)
  covalent geometry    : bond        0.00365 ( 4933)
  covalent geometry    : angle       0.72538 ( 6693)

*********************** 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
  143 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8562 (p0) cc_final: 0.7885 (p0)
REVERT: A  102 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: B   36 TYR cc_start: 0.7760 (m-80) cc_final: 0.7060 (m-10)
REVERT: B   61 ARG cc_start: 0.7926 (ptt180) cc_final: 0.7668 (ptt180)
REVERT: B   83 PHE cc_start: 0.7797 (m-80) cc_final: 0.7467 (m-80)
REVERT: C   22 MET cc_start: 0.8637 (mmp) cc_final: 0.8420 (mmp)
  outliers start: 19
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1491
  time to fit residues: 25.4826
Evaluate side-chains
  124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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 37 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0670
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.9522

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.108213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.088649 restraints weight = 10352.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.091745 restraints weight = 6430.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.094005 restraints weight = 4582.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4939  Z= 0.169
  Angle     :  0.689  10.753   6707  Z= 0.346
  Chirality :  0.045   0.176    725
  Planarity :  0.004   0.039    857
  Dihedral  :  4.956  29.233    712
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.48 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.33), residues: 604
  helix:  0.89 (0.59), residues: 77
  sheet:  1.09 (0.33), residues: 223
  loop :  0.05 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  35 
 HIS   0.005   0.002   HIS L  29 
 PHE   0.017   0.002   PHE L  60 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.004   0.001   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00148 (    1)
  link_NAG-ASN         : angle       1.06524 (    3)
  link_BETA1-4         : bond        0.00053 (    1)
  link_BETA1-4         : angle       1.14747 (    3)
  hydrogen bonds       : bond        0.03790 (  200)
  hydrogen bonds       : angle       5.49633 (  525)
  SS BOND              : bond        0.00197 (    4)
  SS BOND              : angle       1.26883 (    8)
  covalent geometry    : bond        0.00402 ( 4933)
  covalent geometry    : angle       0.68790 ( 6693)

*********************** 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
  126 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8647 (p0) cc_final: 0.7892 (p0)
REVERT: A  102 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: B   36 TYR cc_start: 0.7801 (m-80) cc_final: 0.7091 (m-10)
REVERT: B   83 PHE cc_start: 0.7857 (m-80) cc_final: 0.7464 (m-80)
REVERT: C  115 GLU cc_start: 0.8038 (mp0) cc_final: 0.7770 (mp0)
  outliers start: 15
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1594
  time to fit residues: 24.5229
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
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   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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.107233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.087845 restraints weight = 10668.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090979 restraints weight = 6730.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.093255 restraints weight = 4812.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4939  Z= 0.146
  Angle     :  0.678  10.557   6707  Z= 0.336
  Chirality :  0.043   0.173    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.804  27.923    712
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 22.67 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.33), residues: 604
  helix:  0.95 (0.60), residues: 77
  sheet:  1.19 (0.33), residues: 219
  loop : -0.09 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.014   0.002   PHE C  91 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    1)
  link_NAG-ASN         : angle       1.16645 (    3)
  link_BETA1-4         : bond        0.00144 (    1)
  link_BETA1-4         : angle       1.21812 (    3)
  hydrogen bonds       : bond        0.03634 (  200)
  hydrogen bonds       : angle       5.39344 (  525)
  SS BOND              : bond        0.00282 (    4)
  SS BOND              : angle       0.94853 (    8)
  covalent geometry    : bond        0.00350 ( 4933)
  covalent geometry    : angle       0.67732 ( 6693)

*********************** 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
  134 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8634 (p0) cc_final: 0.7795 (p0)
REVERT: B   83 PHE cc_start: 0.7825 (m-80) cc_final: 0.7182 (m-80)
REVERT: B   87 TYR cc_start: 0.8292 (m-80) cc_final: 0.7847 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 126
  average time/residue: 0.1644
  time to fit residues: 26.3940
Evaluate side-chains
  113 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
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 C residue   49 VAL
Chi-restraints excluded: chain C residue   58 TYR
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 L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
L  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.106853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.087296 restraints weight = 10571.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.090473 restraints weight = 6598.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.092841 restraints weight = 4708.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3348

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= 0.150
  Angle     :  0.692  10.446   6707  Z= 0.341
  Chirality :  0.044   0.170    725
  Planarity :  0.004   0.035    857
  Dihedral  :  4.792  26.883    712
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 23.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.34), residues: 604
  helix:  0.97 (0.61), residues: 77
  sheet:  1.28 (0.33), residues: 218
  loop : -0.02 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.013   0.002   PHE B  83 
 TYR   0.019   0.002   TYR L  85 
 ARG   0.003   0.000   ARG L  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.05013 (    3)
  link_BETA1-4         : bond        0.00044 (    1)
  link_BETA1-4         : angle       1.16154 (    3)
  hydrogen bonds       : bond        0.03515 (  200)
  hydrogen bonds       : angle       5.31800 (  525)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.79209 (    8)
  covalent geometry    : bond        0.00358 ( 4933)
  covalent geometry    : angle       0.69130 ( 6693)

*********************** 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
  127 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7120 (mm-40)
REVERT: A   56 ASP cc_start: 0.8617 (p0) cc_final: 0.7785 (p0)
REVERT: A  102 GLU cc_start: 0.8563 (tp30) cc_final: 0.8322 (tm-30)
REVERT: B   87 TYR cc_start: 0.8288 (m-80) cc_final: 0.7818 (m-80)
REVERT: C  124 MET cc_start: 0.8639 (mtt) cc_final: 0.8417 (mtt)
  outliers start: 18
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1573
  time to fit residues: 24.1746
Evaluate side-chains
  116 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
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 57 optimal weight:    0.7980
   chunk 49 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0470
   chunk 41 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.0880

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.105210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085152 restraints weight = 10691.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.088310 restraints weight = 6740.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.090650 restraints weight = 4848.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4939  Z= 0.181
  Angle     :  0.697  11.676   6707  Z= 0.343
  Chirality :  0.043   0.170    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.905  26.989    712
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 24.22 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.34), residues: 604
  helix:  0.89 (0.60), residues: 77
  sheet:  1.29 (0.33), residues: 212
  loop : -0.10 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  35 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.015   0.002   PHE C 117 
 TYR   0.020   0.002   TYR L  85 
 ARG   0.004   0.000   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    1)
  link_NAG-ASN         : angle       1.03910 (    3)
  link_BETA1-4         : bond        0.00029 (    1)
  link_BETA1-4         : angle       1.16962 (    3)
  hydrogen bonds       : bond        0.03549 (  200)
  hydrogen bonds       : angle       5.33296 (  525)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.79096 (    8)
  covalent geometry    : bond        0.00434 ( 4933)
  covalent geometry    : angle       0.69677 ( 6693)

*********************** 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
  127 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8662 (p0) cc_final: 0.7799 (p0)
REVERT: C  124 MET cc_start: 0.8664 (mtt) cc_final: 0.8460 (mtt)
  outliers start: 22
  outliers final: 20
  residues processed: 120
  average time/residue: 0.1580
  time to fit residues: 24.5409
Evaluate side-chains
  123 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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   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   80 GLN
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  117 TYR
Chi-restraints excluded: chain L residue   35 GLN
Chi-restraints excluded: chain L residue   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
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 11 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 53 optimal weight:    0.1980
   chunk 42 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.107146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.087353 restraints weight = 10615.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.090489 restraints weight = 6785.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.092807 restraints weight = 4884.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4939  Z= 0.133
  Angle     :  0.691  10.235   6707  Z= 0.340
  Chirality :  0.044   0.163    725
  Planarity :  0.004   0.038    857
  Dihedral  :  4.805  25.964    712
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.61 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.34), residues: 604
  helix:  0.54 (0.59), residues: 77
  sheet:  1.30 (0.34), residues: 207
  loop : -0.10 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  35 
 HIS   0.003   0.001   HIS L  29 
 PHE   0.017   0.002   PHE A  81 
 TYR   0.020   0.002   TYR B  36 
 ARG   0.008   0.000   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       0.89039 (    3)
  link_BETA1-4         : bond        0.00248 (    1)
  link_BETA1-4         : angle       1.25083 (    3)
  hydrogen bonds       : bond        0.03477 (  200)
  hydrogen bonds       : angle       5.23137 (  525)
  SS BOND              : bond        0.00305 (    4)
  SS BOND              : angle       0.71771 (    8)
  covalent geometry    : bond        0.00321 ( 4933)
  covalent geometry    : angle       0.69073 ( 6693)

*********************** 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
  138 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ASP cc_start: 0.8578 (p0) cc_final: 0.7661 (p0)
REVERT: A   66 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6917 (tppt)
REVERT: B   87 TYR cc_start: 0.8338 (m-80) cc_final: 0.8069 (m-80)
  outliers start: 24
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1512
  time to fit residues: 25.1489
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  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  116 THR
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   80 GLN
Chi-restraints excluded: chain C residue   85 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
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   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 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 57 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   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 = 0.3521 r_free = 0.3521 target = 0.105310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.085358 restraints weight = 10637.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.088478 restraints weight = 6764.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.090806 restraints weight = 4863.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3828

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= 0.166
  Angle     :  0.713  11.182   6707  Z= 0.353
  Chirality :  0.044   0.167    725
  Planarity :  0.004   0.036    857
  Dihedral  :  4.885  25.076    712
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.31 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.58 %
    Favored  : 70.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.34), residues: 604
  helix:  0.70 (0.59), residues: 77
  sheet:  1.29 (0.34), residues: 207
  loop : -0.17 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  35 
 HIS   0.003   0.001   HIS L  29 
 PHE   0.014   0.002   PHE H 107 
 TYR   0.020   0.002   TYR L  85 
 ARG   0.005   0.000   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       0.88047 (    3)
  link_BETA1-4         : bond        0.00051 (    1)
  link_BETA1-4         : angle       1.11614 (    3)
  hydrogen bonds       : bond        0.03638 (  200)
  hydrogen bonds       : angle       5.16542 (  525)
  SS BOND              : bond        0.00221 (    4)
  SS BOND              : angle       0.76705 (    8)
  covalent geometry    : bond        0.00401 ( 4933)
  covalent geometry    : angle       0.71268 ( 6693)

*********************** 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
  126 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6847 (tppt)
REVERT: A   81 PHE cc_start: 0.8359 (m-80) cc_final: 0.7958 (m-10)
REVERT: A  104 TYR cc_start: 0.8344 (m-80) cc_final: 0.7969 (m-80)
REVERT: B   87 TYR cc_start: 0.8475 (m-80) cc_final: 0.8188 (m-80)
REVERT: C   22 MET cc_start: 0.8391 (mmp) cc_final: 0.8034 (mmp)
  outliers start: 20
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1482
  time to fit residues: 23.0020
Evaluate side-chains
  118 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  116 THR
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   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
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   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN
A  41 GLN
B  90 HIS
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.102469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.081957 restraints weight = 10851.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.084999 restraints weight = 6944.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.087257 restraints weight = 5065.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   4939  Z= 0.229
  Angle     :  0.748  10.357   6707  Z= 0.376
  Chirality :  0.045   0.169    725
  Planarity :  0.004   0.037    857
  Dihedral  :  5.275  24.419    712
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 19.39
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.30 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 25.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.33), residues: 604
  helix:  0.45 (0.58), residues: 77
  sheet:  1.08 (0.34), residues: 215
  loop : -0.37 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  35 
 HIS   0.003   0.001   HIS L  29 
 PHE   0.018   0.003   PHE C 117 
 TYR   0.018   0.002   TYR L  85 
 ARG   0.005   0.001   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    1)
  link_NAG-ASN         : angle       1.03686 (    3)
  link_BETA1-4         : bond        0.00150 (    1)
  link_BETA1-4         : angle       1.03220 (    3)
  hydrogen bonds       : bond        0.03861 (  200)
  hydrogen bonds       : angle       5.30461 (  525)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       0.79412 (    8)
  covalent geometry    : bond        0.00546 ( 4933)
  covalent geometry    : angle       0.74747 ( 6693)

********************** 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
  125 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6814 (tppt)
REVERT: A  104 TYR cc_start: 0.8465 (m-80) cc_final: 0.8119 (m-80)
REVERT: B   87 TYR cc_start: 0.8563 (m-80) cc_final: 0.8247 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 117
  average time/residue: 0.1561
  time to fit residues: 23.4722
Evaluate side-chains
  117 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue   28 SER
Chi-restraints excluded: chain A residue   66 LYS
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   54 LEU
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   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  105 LEU
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   86 CYS
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue   98 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.102212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.082292 restraints weight = 10802.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.085281 restraints weight = 6933.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.087494 restraints weight = 5031.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.4185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.120   4939  Z= 0.290
  Angle     :  1.233  59.192   6707  Z= 0.694
  Chirality :  0.046   0.332    725
  Planarity :  0.005   0.042    857
  Dihedral  :  5.275  24.312    712
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 21.81
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.30 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 27.13 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.33), residues: 604
  helix:  0.45 (0.58), residues: 77
  sheet:  1.06 (0.33), residues: 215
  loop : -0.41 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  49 
 HIS   0.004   0.001   HIS L  29 
 PHE   0.017   0.002   PHE C  91 
 TYR   0.017   0.002   TYR L  85 
 ARG   0.004   0.001   ARG H 100 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00393 (    1)
  link_NAG-ASN         : angle       1.03420 (    3)
  link_BETA1-4         : bond        0.00221 (    1)
  link_BETA1-4         : angle       1.30360 (    3)
  hydrogen bonds       : bond        0.03825 (  200)
  hydrogen bonds       : angle       5.29859 (  525)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       0.76653 (    8)
  covalent geometry    : bond        0.00662 ( 4933)
  covalent geometry    : angle       1.23350 ( 6693)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1981.59 seconds
wall clock time: 37 minutes 3.82 seconds (2223.82 seconds total)