Starting phenix.real_space_refine
on Tue Feb 11 06:38:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uaq_26430/02_2025/7uaq_26430.cif"
  }
  resolution = 3.1
  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=  -0.003 sd=   0.035
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      16      5.16       5
     C    2773      2.51       5
     N     723      2.21       5
     O     850      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4362
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2392
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 15, 'TRANS': 279}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 997
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 833
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 107}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      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
    Chain: "C"
      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
    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
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "L"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.87, per 1000 atoms: 0.89
  Number of scatterers: 4362
  At special positions: 0
  Unit cell: (96.82, 64.89, 89.61, 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      16     16.00
     O     850      8.00
     N     723      7.00
     C    2773      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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 B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A  61 "
      " NAG A1302 " - " ASN A 165 "
      " NAG A1303 " - " ASN A 282 "
      " NAG B   1 " - " ASN A 122 "
      " NAG C   1 " - " ASN A 149 "
      " NAG D   1 " - " ASN A 234 "
      " NAG L 301 " - " ASN L  20 "
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 475.1 milliseconds
  

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 12 sheets defined
      4.9% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.625A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 26 through 29
      removed outlier: 3.625A  pdb=" N   ASN L  29 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.628A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLU L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 4.319A  pdb=" N   ALA A  27 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55
      removed outlier: 3.501A  pdb=" N   LYS A 278 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104
      removed outlier: 6.301A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117
    Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.693A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER H   7 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU H  20 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39
      removed outlier: 7.162A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89
      removed outlier: 3.612A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 119 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95
      removed outlier: 3.936A  pdb=" N   ILE H 112 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.524A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER L  67 " --> pdb=" O   GLU L  70 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50
      removed outlier: 6.653A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   SER L  49 " --> pdb=" O   ILE L  33 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ILE L  33 " --> pdb=" O   SER L  49 " (cutoff:3.500A)

    91 hydrogen bonds defined for protein.
    231 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: 1.05

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1293
        1.34 -     1.46: 1224
        1.46 -     1.59: 1933
        1.59 -     1.72: 0
        1.72 -     1.84: 22
  Bond restraints: 4472
  Sorted by residual:
  bond pdb=" N   ILE A 233 "
       pdb=" CA  ILE A 233 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.15e-02 7.56e+03 1.02e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.467 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" N   ILE A 197 "
       pdb=" CA  ILE A 197 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.18e-02 7.18e+03 8.87e+00
  bond pdb=" N   ILE A  68 "
       pdb=" CA  ILE A  68 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 6.85e+00
  bond pdb=" N   GLY L 101 "
       pdb=" CA  GLY L 101 "
    ideal  model  delta    sigma   weight residual
    1.447  1.474 -0.027 1.09e-02 8.42e+03 6.11e+00
  ... (remaining 4467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 5766
        2.49 -     4.99: 266
        4.99 -     7.48: 28
        7.48 -     9.98: 11
        9.98 -    12.47: 2
  Bond angle restraints: 6073
  Sorted by residual:
  angle pdb=" C   ASN A 165 "
        pdb=" CA  ASN A 165 "
        pdb=" CB  ASN A 165 "
      ideal   model   delta    sigma   weight residual
     110.42  122.89  -12.47 1.99e+00 2.53e-01 3.93e+01
  angle pdb=" N   ASN A 122 "
        pdb=" CA  ASN A 122 "
        pdb=" CB  ASN A 122 "
      ideal   model   delta    sigma   weight residual
     110.45  101.66    8.79 1.44e+00 4.82e-01 3.73e+01
  angle pdb=" CA  GLY L 101 "
        pdb=" C   GLY L 101 "
        pdb=" O   GLY L 101 "
      ideal   model   delta    sigma   weight residual
     122.29  117.98    4.31 8.10e-01 1.52e+00 2.83e+01
  angle pdb=" N   ASN A 165 "
        pdb=" CA  ASN A 165 "
        pdb=" CB  ASN A 165 "
      ideal   model   delta    sigma   weight residual
     110.49  101.68    8.81 1.69e+00 3.50e-01 2.72e+01
  angle pdb=" N   ASN L  20 "
        pdb=" CA  ASN L  20 "
        pdb=" CB  ASN L  20 "
      ideal   model   delta    sigma   weight residual
     110.84  104.20    6.64 1.52e+00 4.33e-01 1.91e+01
  ... (remaining 6068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.78: 2435
       14.78 -    29.56: 219
       29.56 -    44.34: 53
       44.34 -    59.13: 28
       59.13 -    73.91: 4
  Dihedral angle restraints: 2739
    sinusoidal: 1197
      harmonic: 1542
  Sorted by residual:
  dihedral pdb=" N   ASN A 122 "
           pdb=" C   ASN A 122 "
           pdb=" CA  ASN A 122 "
           pdb=" CB  ASN A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.48   12.32     0      2.50e+00 1.60e-01 2.43e+01
  dihedral pdb=" CA  GLN H  81 "
           pdb=" C   GLN H  81 "
           pdb=" N   MET H  82 "
           pdb=" CA  MET H  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  HIS L  54B"
           pdb=" C   HIS L  54B"
           pdb=" N   THR L  54C"
           pdb=" CA  THR L  54C"
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.31   19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 2736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 537
       0.078 -    0.155: 128
       0.155 -    0.233: 15
       0.233 -    0.310: 3
       0.310 -    0.388: 4
  Chirality restraints: 687
  Sorted by residual:
  chirality pdb=" C4  NAG C   1 "
            pdb=" C3  NAG C   1 "
            pdb=" C5  NAG C   1 "
            pdb=" O4  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.14   -0.39 2.00e-01 2.50e+01 3.76e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 149 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.75    0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" C1  NAG A1302 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG A1302 "
            pdb=" O5  NAG A1302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.97e+00
  ... (remaining 684 not shown)

  Planarity restraints: 773
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 165 "    0.010 2.00e-02 2.50e+03   7.50e-02 7.02e+01
        pdb=" CG  ASN A 165 "   -0.093 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 165 "    0.089 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 165 "   -0.078 2.00e-02 2.50e+03
        pdb=" C1  NAG A1302 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 224 "    0.085 5.00e-02 4.00e+02   1.29e-01 2.64e+01
        pdb=" N   PRO A 225 "   -0.222 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "    0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 165 "    0.023 2.00e-02 2.50e+03   4.56e-02 2.08e+01
        pdb=" CG  ASN A 165 "   -0.079 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 165 "    0.030 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 165 "    0.026 2.00e-02 2.50e+03
  ... (remaining 770 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 125
        2.66 -     3.22: 4192
        3.22 -     3.78: 6567
        3.78 -     4.34: 9038
        4.34 -     4.90: 14761
  Nonbonded interactions: 34683
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" OG1 THR L 102 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OG1 THR L  22 "
            pdb=" OE2 GLU L  70 "
     model   vdw
     2.102 3.040
  nonbonded pdb=" OE2 GLU A  96 "
            pdb=" N   ASN A  99 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" O   SER H  30 "
            pdb=" OG1 THR H  52A"
     model   vdw
     2.174 3.040
  nonbonded pdb=" OE1 GLN A  14 "
            pdb=" NH1 ARG A 158 "
     model   vdw
     2.210 3.120
  ... (remaining 34678 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.810
  Find NCS groups from input model:        0.050
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
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      :  0.006   0.061   4472  Z= 0.399
  Angle     :  1.187  12.470   6073  Z= 0.662
  Chirality :  0.071   0.388    687
  Planarity :  0.008   0.129    766
  Dihedral  : 13.129  73.906   1740
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 25.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.47 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.86 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.41 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.35), residues: 523
  helix: -0.03 (1.56), residues: 11
  sheet: -0.76 (0.46), residues: 139
  loop : -2.30 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 152 
 HIS   0.008   0.002   HIS H 106 
 PHE   0.032   0.003   PHE L  72 
 TYR   0.032   0.002   TYR A 144 
 ARG   0.007   0.001   ARG A 319 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8027 (tm-30)
REVERT: A  158 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8067 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8320 (p0) cc_final: 0.8032 (p0)
REVERT: A  314 GLN cc_start: 0.6398 (tp40) cc_final: 0.6067 (tp40)
REVERT: H   38 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6051 (ttm-80)
REVERT: H   67 PHE cc_start: 0.7819 (m-80) cc_final: 0.7310 (m-80)
REVERT: H   97 TYR cc_start: 0.7891 (t80) cc_final: 0.7566 (t80)
REVERT: L   72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6951 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1588
  time to fit residues: 26.5932
Evaluate side-chains
  87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  49 HIS
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 185 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.117200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.093275 restraints weight = 10770.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 4.97
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   4472  Z= 0.297
  Angle     :  0.868  11.774   6073  Z= 0.442
  Chirality :  0.055   0.355    687
  Planarity :  0.006   0.067    766
  Dihedral  :  8.570  57.436    794
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 15.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.74 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.34), residues: 523
  helix:  0.89 (1.65), residues: 11
  sheet: -0.70 (0.43), residues: 145
  loop : -2.23 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  35 
 HIS   0.006   0.002   HIS H  98 
 PHE   0.025   0.002   PHE A 238 
 TYR   0.026   0.002   TYR H  50 
 ARG   0.007   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: A  190 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7470 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8689 (p0) cc_final: 0.8454 (p0)
REVERT: A  298 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6341 (pt0)
REVERT: A  314 GLN cc_start: 0.6845 (tp40) cc_final: 0.6338 (tp40)
REVERT: H  107 SER cc_start: 0.7248 (p) cc_final: 0.6807 (p)
REVERT: L    4 LEU cc_start: 0.7529 (pt) cc_final: 0.7153 (pt)
REVERT: L   85 ASP cc_start: 0.7639 (m-30) cc_final: 0.7004 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1895
  time to fit residues: 25.8764
Evaluate side-chains
  101 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.114475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.090290 restraints weight = 10880.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 5.02
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4472  Z= 0.295
  Angle     :  0.785   9.252   6073  Z= 0.399
  Chirality :  0.051   0.325    687
  Planarity :  0.005   0.051    766
  Dihedral  :  7.965  56.999    792
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 14.25 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.35), residues: 523
  helix:  1.37 (1.83), residues: 11
  sheet: -0.50 (0.44), residues: 147
  loop : -2.13 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L  91 
 HIS   0.005   0.002   HIS A  66 
 PHE   0.014   0.002   PHE A 238 
 TYR   0.021   0.002   TYR H  50 
 ARG   0.008   0.001   ARG L 103 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A  132 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7381 (tm-30)
REVERT: A  190 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7641 (mtt-85)
REVERT: A  314 GLN cc_start: 0.6933 (tp40) cc_final: 0.6640 (tp40)
REVERT: H   45 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8019 (pp)
REVERT: H  107 SER cc_start: 0.7299 (p) cc_final: 0.6947 (p)
REVERT: L    4 LEU cc_start: 0.7592 (pt) cc_final: 0.7246 (pt)
REVERT: L   39 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7574 (tm-30)
REVERT: L   42 LYS cc_start: 0.8533 (mppt) cc_final: 0.7896 (mmtm)
REVERT: L   70 GLU cc_start: 0.7818 (pp20) cc_final: 0.7253 (pp20)
REVERT: L   72 PHE cc_start: 0.7428 (m-80) cc_final: 0.6744 (t80)
REVERT: L   85 ASP cc_start: 0.7714 (m-30) cc_final: 0.7436 (m-30)
  outliers start: 18
  outliers final: 15
  residues processed: 107
  average time/residue: 0.1773
  time to fit residues: 23.8123
Evaluate side-chains
  108 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  106 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 185 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
** H   3 GLN ** 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 = 0.3920 r_free = 0.3920 target = 0.112071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.088159 restraints weight = 10978.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 5.00
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   4472  Z= 0.300
  Angle     :  0.748   9.300   6073  Z= 0.379
  Chirality :  0.051   0.330    687
  Planarity :  0.005   0.050    766
  Dihedral  :  7.529  56.673    792
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.94 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 13.39 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.35), residues: 523
  helix: -1.06 (1.42), residues: 17
  sheet: -0.54 (0.43), residues: 152
  loop : -2.10 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  36 
 HIS   0.006   0.002   HIS A  66 
 PHE   0.013   0.002   PHE A 168 
 TYR   0.023   0.002   TYR H  50 
 ARG   0.005   0.001   ARG L 103 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: A  132 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: A  156 GLU cc_start: 0.2777 (mp0) cc_final: 0.2498 (mp0)
REVERT: A  185 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7640 (p0)
REVERT: A  190 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7743 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8691 (p0) cc_final: 0.8423 (p0)
REVERT: A  314 GLN cc_start: 0.7087 (tp40) cc_final: 0.6793 (tp40)
REVERT: H   45 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7990 (pp)
REVERT: H   57 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.7942 (mmt-90)
REVERT: H   72 ASP cc_start: 0.7301 (p0) cc_final: 0.6985 (p0)
REVERT: H   94 ARG cc_start: 0.8737 (tmm160) cc_final: 0.8478 (tmm-80)
REVERT: L    4 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7356 (pt)
REVERT: L   39 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7686 (tm-30)
REVERT: L   42 LYS cc_start: 0.8551 (mppt) cc_final: 0.7921 (mmtm)
REVERT: L   45 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7190 (ttp-110)
REVERT: L   70 GLU cc_start: 0.7892 (pp20) cc_final: 0.6994 (pp20)
REVERT: L  103 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8193 (mmm160)
  outliers start: 26
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1880
  time to fit residues: 27.1649
Evaluate side-chains
  114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  185 ASN
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0870
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.113451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.089252 restraints weight = 11001.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 5.03
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4472  Z= 0.224
  Angle     :  0.720   9.360   6073  Z= 0.364
  Chirality :  0.049   0.308    687
  Planarity :  0.005   0.048    766
  Dihedral  :  7.330  56.620    792
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.75 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 16.63 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.35), residues: 523
  helix:  1.48 (1.85), residues: 11
  sheet: -0.56 (0.44), residues: 147
  loop : -1.99 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.005   0.001   HIS H  98 
 PHE   0.011   0.002   PHE A 318 
 TYR   0.020   0.002   TYR H 108 
 ARG   0.004   0.000   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: A  115 GLN cc_start: 0.8778 (mm110) cc_final: 0.8526 (mm-40)
REVERT: A  132 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7675 (tm-30)
REVERT: A  190 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7620 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8789 (p0) cc_final: 0.8506 (p0)
REVERT: A  298 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6317 (pt0)
REVERT: A  314 GLN cc_start: 0.7065 (tp40) cc_final: 0.6773 (tp40)
REVERT: H   57 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.7885 (mmt-90)
REVERT: L    4 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7268 (pt)
REVERT: L   39 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7618 (tm-30)
REVERT: L   45 ARG cc_start: 0.7441 (mtm110) cc_final: 0.7172 (ttp-110)
REVERT: L   70 GLU cc_start: 0.7931 (pp20) cc_final: 0.7302 (pp20)
REVERT: L  103 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8171 (mmm160)
  outliers start: 23
  outliers final: 16
  residues processed: 114
  average time/residue: 0.1720
  time to fit residues: 24.4923
Evaluate side-chains
  114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.109907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.085462 restraints weight = 10837.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 4.96
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   4472  Z= 0.307
  Angle     :  0.737   9.333   6073  Z= 0.375
  Chirality :  0.050   0.371    687
  Planarity :  0.005   0.051    766
  Dihedral  :  7.385  56.065    792
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.13 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 17.71 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.35), residues: 523
  helix:  1.61 (1.90), residues: 11
  sheet: -0.62 (0.42), residues: 156
  loop : -2.03 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 258 
 HIS   0.005   0.002   HIS H  98 
 PHE   0.010   0.002   PHE A 168 
 TYR   0.017   0.002   TYR H  50 
 ARG   0.004   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: A  115 GLN cc_start: 0.8882 (mm110) cc_final: 0.8637 (mm-40)
REVERT: A  190 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7576 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8780 (p0) cc_final: 0.8529 (p0)
REVERT: A  314 GLN cc_start: 0.7169 (tp40) cc_final: 0.6913 (tp40)
REVERT: H   57 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.7982 (mmt-90)
REVERT: H  100 TYR cc_start: 0.9374 (m-80) cc_final: 0.9146 (m-10)
REVERT: H  115 GLN cc_start: 0.8705 (mp10) cc_final: 0.8481 (mp10)
REVERT: L    4 LEU cc_start: 0.7642 (pt) cc_final: 0.7352 (pt)
REVERT: L   39 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7690 (tm-30)
REVERT: L   45 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7369 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8099 (pp20) cc_final: 0.7387 (pp20)
REVERT: L  103 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8219 (mmm160)
  outliers start: 19
  outliers final: 17
  residues processed: 105
  average time/residue: 0.1775
  time to fit residues: 23.4200
Evaluate side-chains
  111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  298 GLU
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   50 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0070
   chunk 47 optimal weight:    0.3980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.112542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.087869 restraints weight = 10809.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 5.07
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4472  Z= 0.200
  Angle     :  0.706   9.426   6073  Z= 0.355
  Chirality :  0.049   0.336    687
  Planarity :  0.004   0.052    766
  Dihedral  :  7.173  56.602    792
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.37 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.44 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.36), residues: 523
  helix:  1.45 (1.87), residues: 11
  sheet: -0.52 (0.44), residues: 149
  loop : -1.89 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  36 
 HIS   0.006   0.001   HIS H  98 
 PHE   0.015   0.001   PHE H  67 
 TYR   0.018   0.002   TYR H  50 
 ARG   0.004   0.000   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: A  115 GLN cc_start: 0.8936 (mm110) cc_final: 0.8679 (mm-40)
REVERT: A  132 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: A  190 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7503 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8779 (p0) cc_final: 0.8508 (p0)
REVERT: A  298 GLU cc_start: 0.6971 (pt0) cc_final: 0.6440 (pt0)
REVERT: A  314 GLN cc_start: 0.7058 (tp40) cc_final: 0.6795 (tp40)
REVERT: H   57 ARG cc_start: 0.8430 (mmt-90) cc_final: 0.7943 (mmt-90)
REVERT: H   76 ASN cc_start: 0.7710 (t0) cc_final: 0.7477 (t0)
REVERT: H  115 GLN cc_start: 0.8697 (mp10) cc_final: 0.8400 (mp10)
REVERT: L    4 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7225 (pt)
REVERT: L   39 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7690 (tm-30)
REVERT: L   45 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7276 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8144 (pp20) cc_final: 0.7548 (pp20)
REVERT: L  103 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8157 (mmm160)
  outliers start: 14
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1679
  time to fit residues: 22.2740
Evaluate side-chains
  110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   79 TYR
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue    4 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 4 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.112636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.088065 restraints weight = 10739.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 5.08
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4472  Z= 0.218
  Angle     :  0.712   9.413   6073  Z= 0.360
  Chirality :  0.049   0.347    687
  Planarity :  0.004   0.050    766
  Dihedral  :  7.077  56.194    792
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.65 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.37), residues: 523
  helix:  1.58 (1.88), residues: 11
  sheet: -0.55 (0.43), residues: 155
  loop : -1.82 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 258 
 HIS   0.005   0.001   HIS H  98 
 PHE   0.010   0.001   PHE A 318 
 TYR   0.017   0.002   TYR H 108 
 ARG   0.005   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: A  115 GLN cc_start: 0.8955 (mm110) cc_final: 0.8686 (mm-40)
REVERT: A  132 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7848 (tm-30)
REVERT: A  190 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7471 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8742 (p0) cc_final: 0.8467 (p0)
REVERT: A  314 GLN cc_start: 0.7055 (tp40) cc_final: 0.6815 (tp40)
REVERT: H   57 ARG cc_start: 0.8452 (mmt-90) cc_final: 0.7976 (mmt-90)
REVERT: H   72 ASP cc_start: 0.8201 (p0) cc_final: 0.7647 (p0)
REVERT: H   76 ASN cc_start: 0.7725 (t0) cc_final: 0.7462 (t0)
REVERT: H   97 TYR cc_start: 0.8495 (t80) cc_final: 0.7803 (t80)
REVERT: H  115 GLN cc_start: 0.8670 (mp10) cc_final: 0.8350 (mp10)
REVERT: L    4 LEU cc_start: 0.7430 (pt) cc_final: 0.7152 (pt)
REVERT: L   39 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7695 (tm-30)
REVERT: L   45 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7369 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8112 (pp20) cc_final: 0.7475 (pp20)
  outliers start: 16
  outliers final: 11
  residues processed: 108
  average time/residue: 0.1711
  time to fit residues: 23.2213
Evaluate side-chains
  112 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.110619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086212 restraints weight = 10877.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 5.02
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4472  Z= 0.298
  Angle     :  0.754  10.297   6073  Z= 0.379
  Chirality :  0.050   0.347    687
  Planarity :  0.005   0.051    766
  Dihedral  :  7.164  56.062    792
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.09 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.36), residues: 523
  helix:  1.69 (1.90), residues: 11
  sheet: -0.63 (0.42), residues: 160
  loop : -1.80 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L  91 
 HIS   0.006   0.002   HIS H 106 
 PHE   0.013   0.002   PHE H  67 
 TYR   0.026   0.002   TYR H  97 
 ARG   0.005   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: A  115 GLN cc_start: 0.8937 (mm110) cc_final: 0.8661 (mm-40)
REVERT: A  173 GLN cc_start: 0.8545 (tp40) cc_final: 0.8105 (tp40)
REVERT: A  190 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7469 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8703 (p0) cc_final: 0.8455 (p0)
REVERT: A  314 GLN cc_start: 0.7108 (tp40) cc_final: 0.6887 (tp40)
REVERT: H   57 ARG cc_start: 0.8476 (mmt-90) cc_final: 0.8025 (mmt-90)
REVERT: H   72 ASP cc_start: 0.8046 (p0) cc_final: 0.7621 (p0)
REVERT: H   76 ASN cc_start: 0.7814 (t0) cc_final: 0.7505 (t0)
REVERT: H  115 GLN cc_start: 0.8659 (mp10) cc_final: 0.8329 (mp10)
REVERT: L    4 LEU cc_start: 0.7427 (pt) cc_final: 0.7134 (pt)
REVERT: L   39 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7785 (tm-30)
REVERT: L   70 GLU cc_start: 0.8202 (pp20) cc_final: 0.7587 (pp20)
  outliers start: 16
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1718
  time to fit residues: 23.6274
Evaluate side-chains
  115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 49 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.112202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.087919 restraints weight = 10689.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 5.00
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4472  Z= 0.223
  Angle     :  0.750  10.363   6073  Z= 0.376
  Chirality :  0.049   0.342    687
  Planarity :  0.004   0.049    766
  Dihedral  :  7.112  56.335    792
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 21.38 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.36), residues: 523
  helix:  1.60 (1.93), residues: 11
  sheet: -0.60 (0.43), residues: 150
  loop : -1.77 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  36 
 HIS   0.006   0.001   HIS H  98 
 PHE   0.011   0.001   PHE A 318 
 TYR   0.017   0.002   TYR H  50 
 ARG   0.004   0.001   ARG H  38 

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

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

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1046 Ramachandran restraints generated.
    523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: A  115 GLN cc_start: 0.8947 (mm110) cc_final: 0.8671 (mm-40)
REVERT: A  173 GLN cc_start: 0.8524 (tp40) cc_final: 0.8097 (tp40)
REVERT: A  190 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7466 (mtt-85)
REVERT: A  211 ASN cc_start: 0.8736 (p0) cc_final: 0.8501 (p0)
REVERT: A  314 GLN cc_start: 0.7030 (tp40) cc_final: 0.6801 (tp40)
REVERT: H   57 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8038 (mmt-90)
REVERT: H   72 ASP cc_start: 0.8018 (p0) cc_final: 0.7625 (p0)
REVERT: H   76 ASN cc_start: 0.7800 (t0) cc_final: 0.7536 (t0)
REVERT: H   99 TYR cc_start: 0.9084 (t80) cc_final: 0.8691 (t80)
REVERT: H  100 TYR cc_start: 0.9183 (m-10) cc_final: 0.8979 (m-80)
REVERT: H  105 TYR cc_start: 0.6880 (m-80) cc_final: 0.6602 (m-80)
REVERT: L    4 LEU cc_start: 0.7221 (pt) cc_final: 0.6948 (pt)
REVERT: L   39 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7771 (tm-30)
REVERT: L   45 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7438 (ttp-110)
REVERT: L   70 GLU cc_start: 0.8190 (pp20) cc_final: 0.7679 (pp20)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1736
  time to fit residues: 23.3864
Evaluate side-chains
  111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  294 ASP
Chi-restraints excluded: chain A residue  315 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   25 LEU
Chi-restraints excluded: chain L residue   45 ARG
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.108735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.084196 restraints weight = 10911.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 5.03
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   4472  Z= 0.363
  Angle     :  0.803   9.909   6073  Z= 0.404
  Chirality :  0.050   0.353    687
  Planarity :  0.005   0.054    766
  Dihedral  :  7.448  55.663    792
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.09 %
    Favored  : 88.72 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.52 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.36), residues: 523
  helix:  1.64 (1.89), residues: 11
  sheet: -0.69 (0.41), residues: 160
  loop : -1.77 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP L  91 
 HIS   0.010   0.002   HIS H 106 
 PHE   0.012   0.002   PHE L  72 
 TYR   0.019   0.002   TYR H  99 
 ARG   0.005   0.001   ARG H  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.43 seconds
wall clock time: 41 minutes 4.66 seconds (2464.66 seconds total)