Starting phenix.real_space_refine
on Tue Feb 11 10:24:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c89_16473/02_2025/8c89_16473_neut.cif"
  }
  resolution = 4.41
  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=   0.009
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      25      5.16       5
     C    3227      2.51       5
     N     862      2.21       5
     O     992      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5106
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 1687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1687
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 13, 'TRANS': 196}
    Chain: "H"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1698
          Classifications: {'peptide': 226}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 211}
    Chain: "L"
      Number of atoms: 1665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1665
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204}
    Chain: "A"
      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: "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
  Time building chain proxies: 4.13, per 1000 atoms: 0.81
  Number of scatterers: 5106
  At special positions: 0
  Unit cell: (68.4, 70.965, 145.35, 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      25     16.00
     O     992      8.00
     N     862      7.00
     C    3227      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " 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 A   1 " - " NAG A   2 "
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A   1 " - " ASN C 343 "
      " NAG B   1 " - " ASN H 102 "
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 611.1 milliseconds
  

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 14 sheets defined
      9.0% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 385 through 389
      removed outlier: 4.044A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP C 389 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 385 through 389'
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.946A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 137 through 143
      removed outlier: 4.097A  pdb=" N   SER H 142 " --> pdb=" O   LYS H 139 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLY H 143 " --> pdb=" O   SER H 140 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 197 through 199
      No H-bonds generated for 'chain 'H' and resid 197 through 199'
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'L' and resid 123 through 129
    Processing helix  chain 'L' and resid 185 through 191
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357
      removed outlier: 3.728A  pdb=" N   ILE C 402 " --> pdb=" O   TYR C 508 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR C 508 " --> pdb=" O   ILE C 402 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C 513 " --> pdb=" O   CYS C 432 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.592A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 7.177A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 120 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL H 119 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA H  97 " --> pdb=" O   GLN H  35 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 46 through 47
      removed outlier: 3.682A  pdb=" N   GLN H  35 " --> pdb=" O   ALA H  97 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA H  97 " --> pdb=" O   GLN H  35 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 18 through 19
    Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.957A  pdb=" N   SER H 130 " --> pdb=" O   LYS H 153 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   VAL H 191 " --> pdb=" O   HIS H 174 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS H 174 " --> pdb=" O   VAL H 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.675A  pdb=" N   THR H 161 " --> pdb=" O   ASN H 209 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 13
      removed outlier: 5.815A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 22
    Processing sheet with id=AB3, first strand: chain 'L' and resid 46 through 47
    Processing sheet with id=AB4, first strand: chain 'L' and resid 118 through 120
      removed outlier: 3.568A  pdb=" N   VAL L 135 " --> pdb=" O   PHE L 120 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER L 176 " --> pdb=" O   THR L 166 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER L 178 " --> pdb=" O   SER L 164 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER L 164 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR L 180 " --> pdb=" O   GLN L 162 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 157
      removed outlier: 3.650A  pdb=" N   TRP L 150 " --> pdb=" O   GLN L 157 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR L 194 " --> pdb=" O   PHE L 211 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   HIS L 200 " --> pdb=" O   SER L 205 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   SER L 205 " --> pdb=" O   HIS L 200 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    294 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: 1.31

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 833
        1.32 -     1.44: 1493
        1.44 -     1.57: 2876
        1.57 -     1.69: 0
        1.69 -     1.82: 30
  Bond restraints: 5232
  Sorted by residual:
  bond pdb=" CZ  ARG L 110 "
       pdb=" NH2 ARG L 110 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.15e+00
  bond pdb=" CD  ARG L 110 "
       pdb=" NE  ARG L 110 "
    ideal  model  delta    sigma   weight residual
    1.458  1.427  0.031 1.40e-02 5.10e+03 4.92e+00
  bond pdb=" CA  SER H 125 "
       pdb=" CB  SER H 125 "
    ideal  model  delta    sigma   weight residual
    1.531  1.496  0.035 1.65e-02 3.67e+03 4.53e+00
  bond pdb=" CA  SER H  55 "
       pdb=" CB  SER H  55 "
    ideal  model  delta    sigma   weight residual
    1.535  1.502  0.033 1.58e-02 4.01e+03 4.29e+00
  bond pdb=" C   GLU H 158 "
       pdb=" N   PRO H 159 "
    ideal  model  delta    sigma   weight residual
    1.332  1.358 -0.027 1.30e-02 5.92e+03 4.24e+00
  ... (remaining 5227 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 6894
        2.57 -     5.14: 210
        5.14 -     7.71: 11
        7.71 -    10.28: 1
       10.28 -    12.85: 1
  Bond angle restraints: 7117
  Sorted by residual:
  angle pdb=" CG  ARG L 110 "
        pdb=" CD  ARG L 110 "
        pdb=" NE  ARG L 110 "
      ideal   model   delta    sigma   weight residual
     112.00  124.85  -12.85 2.20e+00 2.07e-01 3.41e+01
  angle pdb=" C   SER H 123 "
        pdb=" N   ALA H 124 "
        pdb=" CA  ALA H 124 "
      ideal   model   delta    sigma   weight residual
     121.70  128.82   -7.12 1.80e+00 3.09e-01 1.56e+01
  angle pdb=" CA  SER H 123 "
        pdb=" C   SER H 123 "
        pdb=" O   SER H 123 "
      ideal   model   delta    sigma   weight residual
     121.89  117.30    4.59 1.17e+00 7.31e-01 1.54e+01
  angle pdb=" C   THR L 111 "
        pdb=" N   VAL L 112 "
        pdb=" CA  VAL L 112 "
      ideal   model   delta    sigma   weight residual
     122.33  116.29    6.04 1.61e+00 3.86e-01 1.41e+01
  angle pdb=" C   THR C 333 "
        pdb=" CA  THR C 333 "
        pdb=" CB  THR C 333 "
      ideal   model   delta    sigma   weight residual
     110.42  117.77   -7.35 1.99e+00 2.53e-01 1.36e+01
  ... (remaining 7112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.29: 3013
       24.29 -    48.58: 144
       48.58 -    72.87: 17
       72.87 -    97.16: 4
       97.16 -   121.46: 3
  Dihedral angle restraints: 3181
    sinusoidal: 1288
      harmonic: 1893
  Sorted by residual:
  dihedral pdb=" CB  CYS H 150 "
           pdb=" SG  CYS H 150 "
           pdb=" SG  CYS H 206 "
           pdb=" CB  CYS H 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.58  -85.58     1      1.00e+01 1.00e-02 8.86e+01
  dihedral pdb=" CA  VAL H  34 "
           pdb=" C   VAL H  34 "
           pdb=" N   GLN H  35 "
           pdb=" CA  GLN H  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.04   38.96     0      5.00e+00 4.00e-02 6.07e+01
  dihedral pdb=" CA  CYS H 101 "
           pdb=" C   CYS H 101 "
           pdb=" N   ASN H 102 "
           pdb=" CA  ASN H 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.12   37.88     0      5.00e+00 4.00e-02 5.74e+01
  ... (remaining 3178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 475
       0.075 -    0.150: 276
       0.150 -    0.224: 39
       0.224 -    0.299: 5
       0.299 -    0.374: 2
  Chirality restraints: 797
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 8.60e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN H 102 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.03   -0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN C 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 794 not shown)

  Planarity restraints: 914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.181 2.00e-02 2.50e+03   1.50e-01 2.80e+02
        pdb=" C7  NAG A   1 "    0.074 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.140 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.232 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.060 2.00e-02 2.50e+03   5.01e-02 3.14e+01
        pdb=" C7  NAG B   1 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "    0.051 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.072 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L 110 "    0.368 9.50e-02 1.11e+02   1.65e-01 1.69e+01
        pdb=" NE  ARG L 110 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  ARG L 110 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG L 110 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG L 110 "    0.011 2.00e-02 2.50e+03
  ... (remaining 911 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 207
        2.70 -     3.25: 5278
        3.25 -     3.80: 8452
        3.80 -     4.35: 10929
        4.35 -     4.90: 17257
  Nonbonded interactions: 42123
  Sorted by model distance:
  nonbonded pdb=" OG  SER H  17 "
            pdb=" OE1 GLU H  82 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" NH1 ARG C 357 "
            pdb=" O   ILE C 358 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" O   ALA C 475 "
            pdb=" N   CYS H 106 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" NE2 GLN L  38 "
            pdb=" O   GLU L  82 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" OH  TYR C 473 "
            pdb=" O   THR H 104 "
     model   vdw
     2.245 3.040
  ... (remaining 42118 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 'A'
  selection = chain 'B'
}

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:             22.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     14.620
  Find NCS groups from input model:        0.090
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
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      :  0.007   0.039   5232  Z= 0.471
  Angle     :  1.101  12.849   7117  Z= 0.677
  Chirality :  0.085   0.374    797
  Planarity :  0.009   0.165    912
  Dihedral  : 14.363 121.455   1944
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 25.75
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.37 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  2.65 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.33 %

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: -2.47 (0.32), residues: 646
  helix: -2.31 (0.83), residues: 28
  sheet: -0.68 (0.36), residues: 217
  loop : -2.25 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.005   TRP C 353 
 HIS   0.007   0.002   HIS L 200 
 PHE   0.032   0.004   PHE H 176 
 TYR   0.030   0.004   TYR L  50 
 ARG   0.007   0.001   ARG L 110 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.522 
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: C  365 TYR cc_start: 0.9052 (m-80) cc_final: 0.8842 (m-80)
REVERT: C  377 PHE cc_start: 0.8966 (t80) cc_final: 0.8669 (t80)
REVERT: C  418 ILE cc_start: 0.9248 (pt) cc_final: 0.9040 (pt)
REVERT: C  429 PHE cc_start: 0.9101 (t80) cc_final: 0.8801 (t80)
REVERT: C  451 TYR cc_start: 0.6961 (m-80) cc_final: 0.6674 (m-80)
REVERT: C  478 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8862 (tmtt)
REVERT: H   10 GLU cc_start: 0.8489 (mp0) cc_final: 0.8243 (pm20)
REVERT: H   73 ASP cc_start: 0.9360 (t0) cc_final: 0.9097 (t0)
REVERT: H   80 TYR cc_start: 0.9387 (m-80) cc_final: 0.9018 (m-80)
REVERT: H   93 MET cc_start: 0.8715 (tpp) cc_final: 0.8322 (tpp)
REVERT: L   37 TYR cc_start: 0.8936 (m-10) cc_final: 0.8720 (m-80)
REVERT: L   88 TYR cc_start: 0.8526 (m-10) cc_final: 0.8064 (m-10)
  outliers start: 4
  outliers final: 3
  residues processed: 147
  average time/residue: 0.2183
  time to fit residues: 39.1488
Evaluate side-chains
  138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 135
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0040
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.2790

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.179990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.143944 restraints weight = 10923.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.150328 restraints weight = 6784.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155214 restraints weight = 4676.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5232  Z= 0.222
  Angle     :  0.721   9.134   7117  Z= 0.372
  Chirality :  0.049   0.223    797
  Planarity :  0.006   0.055    912
  Dihedral  : 10.813 112.272    796
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.29 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -2.21 (0.32), residues: 646
  helix: -1.91 (0.90), residues: 28
  sheet: -0.58 (0.35), residues: 226
  loop : -2.07 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 353 
 HIS   0.006   0.002   HIS L 191 
 PHE   0.017   0.002   PHE H 176 
 TYR   0.020   0.002   TYR C 351 
 ARG   0.007   0.001   ARG C 466 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7412 (mmm160)
REVERT: C  357 ARG cc_start: 0.7254 (tpt90) cc_final: 0.6891 (tpt90)
REVERT: C  358 ILE cc_start: 0.7154 (mp) cc_final: 0.6940 (mp)
REVERT: C  392 PHE cc_start: 0.6858 (m-10) cc_final: 0.6558 (m-10)
REVERT: C  398 ASP cc_start: 0.6238 (p0) cc_final: 0.5455 (p0)
REVERT: C  418 ILE cc_start: 0.8658 (pt) cc_final: 0.8348 (pt)
REVERT: C  423 TYR cc_start: 0.7874 (t80) cc_final: 0.7391 (t80)
REVERT: C  429 PHE cc_start: 0.8059 (t80) cc_final: 0.7590 (t80)
REVERT: C  451 TYR cc_start: 0.6302 (m-80) cc_final: 0.5777 (m-80)
REVERT: C  478 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8537 (tmtt)
REVERT: H   10 GLU cc_start: 0.7764 (mp0) cc_final: 0.7457 (mp0)
REVERT: H   38 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7444 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8663 (pm20) cc_final: 0.8258 (pm20)
REVERT: H   64 PHE cc_start: 0.8431 (m-10) cc_final: 0.8163 (m-10)
REVERT: H   73 ASP cc_start: 0.8562 (t0) cc_final: 0.7571 (t0)
REVERT: H   80 TYR cc_start: 0.6679 (m-80) cc_final: 0.6099 (m-80)
REVERT: H   93 MET cc_start: 0.8360 (tpp) cc_final: 0.8126 (tpp)
REVERT: H   94 TYR cc_start: 0.7733 (m-10) cc_final: 0.7465 (m-10)
REVERT: H  187 SER cc_start: 0.8140 (p) cc_final: 0.7821 (t)
REVERT: L   13 LEU cc_start: 0.8488 (tp) cc_final: 0.8206 (tp)
REVERT: L   86 MET cc_start: 0.6683 (tpp) cc_final: 0.6124 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2136
  time to fit residues: 36.2317
Evaluate side-chains
  130 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.173101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.138245 restraints weight = 11093.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.144710 restraints weight = 6857.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.149261 restraints weight = 4623.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   5232  Z= 0.360
  Angle     :  0.775   8.112   7117  Z= 0.410
  Chirality :  0.051   0.231    797
  Planarity :  0.006   0.057    912
  Dihedral  : 10.865 113.483    796
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 27.34
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.61 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.55 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -2.17 (0.33), residues: 646
  helix: -2.46 (0.79), residues: 28
  sheet: -0.34 (0.36), residues: 214
  loop : -2.09 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C 353 
 HIS   0.005   0.002   HIS L 191 
 PHE   0.018   0.002   PHE C 490 
 TYR   0.023   0.002   TYR L  50 
 ARG   0.011   0.001   ARG L  62 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7794 (m110) cc_final: 0.7537 (m110)
REVERT: C  378 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8697 (tmmt)
REVERT: C  392 PHE cc_start: 0.6946 (m-10) cc_final: 0.6502 (m-10)
REVERT: C  418 ILE cc_start: 0.8741 (pt) cc_final: 0.8468 (pt)
REVERT: C  423 TYR cc_start: 0.7854 (t80) cc_final: 0.7336 (t80)
REVERT: C  429 PHE cc_start: 0.8129 (t80) cc_final: 0.7561 (t80)
REVERT: C  451 TYR cc_start: 0.6086 (m-80) cc_final: 0.5681 (m-80)
REVERT: C  457 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7381 (ttp80)
REVERT: C  478 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8537 (tmtt)
REVERT: H   10 GLU cc_start: 0.7868 (mp0) cc_final: 0.7459 (mp0)
REVERT: H   38 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7744 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8768 (pm20) cc_final: 0.8206 (pm20)
REVERT: H   64 PHE cc_start: 0.8553 (m-10) cc_final: 0.8229 (m-10)
REVERT: H   73 ASP cc_start: 0.8655 (t0) cc_final: 0.7477 (t0)
REVERT: H   80 TYR cc_start: 0.6777 (m-80) cc_final: 0.6183 (m-80)
REVERT: H   93 MET cc_start: 0.8507 (tpp) cc_final: 0.8297 (tpp)
REVERT: L   13 LEU cc_start: 0.8745 (tp) cc_final: 0.8352 (tp)
REVERT: L   49 ILE cc_start: 0.4290 (mp) cc_final: 0.4054 (mp)
REVERT: L   86 MET cc_start: 0.7061 (tpp) cc_final: 0.6508 (tpp)
REVERT: L  142 TYR cc_start: 0.7360 (t80) cc_final: 0.7075 (t80)
REVERT: L  174 THR cc_start: 0.7070 (m) cc_final: 0.6725 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2169
  time to fit residues: 39.3861
Evaluate side-chains
  137 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.0050
   chunk 25 optimal weight:    0.5980
   chunk 6 optimal weight:    0.4980
   chunk 47 optimal weight:    0.0470
   chunk 3 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0570
   chunk 14 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.1210

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

Flipped N/Q/H residues before XYZ refinement:
C 505 HIS
** L   6 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 = 0.4483 r_free = 0.4483 target = 0.181112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.145327 restraints weight = 11459.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.152308 restraints weight = 7178.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.157269 restraints weight = 4862.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5232  Z= 0.180
  Angle     :  0.706   8.817   7117  Z= 0.360
  Chirality :  0.049   0.226    797
  Planarity :  0.005   0.053    912
  Dihedral  :  9.788 104.681    796
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.05 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.70 %
    Twisted General : 0.16 %

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: -1.96 (0.33), residues: 646
  helix: -2.32 (0.85), residues: 28
  sheet: -0.00 (0.37), residues: 211
  loop : -2.07 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.005   0.002   HIS C 519 
 PHE   0.017   0.002   PHE C 464 
 TYR   0.015   0.002   TYR C 351 
 ARG   0.005   0.001   ARG L  55 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  392 PHE cc_start: 0.6973 (m-10) cc_final: 0.6600 (m-10)
REVERT: C  418 ILE cc_start: 0.8561 (pt) cc_final: 0.8335 (pt)
REVERT: C  429 PHE cc_start: 0.8134 (t80) cc_final: 0.7613 (t80)
REVERT: C  451 TYR cc_start: 0.6230 (m-80) cc_final: 0.5785 (m-80)
REVERT: C  455 LEU cc_start: 0.5968 (mt) cc_final: 0.5743 (mt)
REVERT: C  457 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7358 (ttp80)
REVERT: H   10 GLU cc_start: 0.7768 (mp0) cc_final: 0.7178 (mp0)
REVERT: H   38 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7710 (tmm-80)
REVERT: H   39 GLN cc_start: 0.7792 (tt0) cc_final: 0.7518 (tt0)
REVERT: H   62 GLN cc_start: 0.8662 (pm20) cc_final: 0.8324 (pm20)
REVERT: H   64 PHE cc_start: 0.8479 (m-10) cc_final: 0.8246 (m-10)
REVERT: H   73 ASP cc_start: 0.8375 (t0) cc_final: 0.7290 (t0)
REVERT: H   80 TYR cc_start: 0.6635 (m-80) cc_final: 0.6164 (m-80)
REVERT: H   94 TYR cc_start: 0.7664 (m-10) cc_final: 0.7463 (m-10)
REVERT: L   13 LEU cc_start: 0.8530 (tp) cc_final: 0.8205 (tp)
REVERT: L  174 THR cc_start: 0.6674 (m) cc_final: 0.6406 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1971
  time to fit residues: 34.0766
Evaluate side-chains
  132 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 422 ASN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 200 HIS ** 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 = 0.4384 r_free = 0.4384 target = 0.172277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.137662 restraints weight = 11200.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.144117 restraints weight = 7015.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.148780 restraints weight = 4762.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6632
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   5232  Z= 0.341
  Angle     :  0.761   8.904   7117  Z= 0.400
  Chirality :  0.049   0.226    797
  Planarity :  0.006   0.053    912
  Dihedral  : 10.003 106.332    796
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 27.24
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.46 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.95 (0.33), residues: 646
  helix: -2.32 (0.83), residues: 28
  sheet: -0.23 (0.36), residues: 217
  loop : -1.92 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.015   0.002   PHE H  29 
 TYR   0.022   0.002   TYR C 380 
 ARG   0.005   0.001   ARG L  55 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8136 (mmm160)
REVERT: C  392 PHE cc_start: 0.6988 (m-10) cc_final: 0.6611 (m-10)
REVERT: C  418 ILE cc_start: 0.8602 (pt) cc_final: 0.8348 (pt)
REVERT: C  429 PHE cc_start: 0.8179 (t80) cc_final: 0.7631 (t80)
REVERT: C  451 TYR cc_start: 0.6099 (m-80) cc_final: 0.5644 (m-80)
REVERT: C  478 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8568 (tmtt)
REVERT: H   10 GLU cc_start: 0.7824 (mp0) cc_final: 0.7084 (mp0)
REVERT: H   38 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7920 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8801 (pm20) cc_final: 0.8193 (pm20)
REVERT: H   64 PHE cc_start: 0.8596 (m-10) cc_final: 0.8306 (m-10)
REVERT: H   73 ASP cc_start: 0.8604 (t0) cc_final: 0.7281 (t0)
REVERT: H   74 MET cc_start: 0.7586 (mmt) cc_final: 0.7235 (mmt)
REVERT: H   76 THR cc_start: 0.8290 (t) cc_final: 0.8054 (t)
REVERT: H   80 TYR cc_start: 0.6617 (m-80) cc_final: 0.6185 (m-80)
REVERT: H   94 TYR cc_start: 0.7815 (m-10) cc_final: 0.7513 (m-10)
REVERT: L   13 LEU cc_start: 0.8714 (tp) cc_final: 0.7651 (tp)
REVERT: L   17 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7008 (mt-10)
REVERT: L   37 TYR cc_start: 0.7811 (m-10) cc_final: 0.7551 (m-80)
REVERT: L   92 TYR cc_start: 0.8152 (p90) cc_final: 0.7719 (p90)
REVERT: L  134 VAL cc_start: 0.8282 (t) cc_final: 0.7923 (p)
REVERT: L  142 TYR cc_start: 0.7275 (t80) cc_final: 0.6927 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2000
  time to fit residues: 35.4633
Evaluate side-chains
  136 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 50 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 10 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0980
   overall best weight:    0.1778

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.4435 r_free = 0.4435 target = 0.177250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.141895 restraints weight = 11184.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.148672 restraints weight = 7065.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.153517 restraints weight = 4817.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5232  Z= 0.202
  Angle     :  0.715   8.708   7117  Z= 0.367
  Chirality :  0.049   0.222    797
  Planarity :  0.006   0.056    912
  Dihedral  :  9.621 103.753    796
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.29 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.87 (0.33), residues: 646
  helix: -2.27 (0.88), residues: 28
  sheet: -0.09 (0.37), residues: 221
  loop : -1.95 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L  91 
 PHE   0.030   0.002   PHE C 515 
 TYR   0.018   0.002   TYR L  50 
 ARG   0.006   0.001   ARG H  38 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8285 (mmm160) cc_final: 0.8056 (mmm160)
REVERT: C  377 PHE cc_start: 0.8716 (t80) cc_final: 0.8253 (t80)
REVERT: C  378 LYS cc_start: 0.8882 (tmmt) cc_final: 0.8600 (tmmt)
REVERT: C  392 PHE cc_start: 0.6956 (m-10) cc_final: 0.6573 (m-10)
REVERT: C  402 ILE cc_start: 0.8416 (tp) cc_final: 0.8203 (tp)
REVERT: C  418 ILE cc_start: 0.8569 (pt) cc_final: 0.8320 (pt)
REVERT: C  422 ASN cc_start: 0.7604 (m110) cc_final: 0.7322 (m110)
REVERT: C  429 PHE cc_start: 0.8175 (t80) cc_final: 0.7631 (t80)
REVERT: C  451 TYR cc_start: 0.6001 (m-80) cc_final: 0.5611 (m-80)
REVERT: C  455 LEU cc_start: 0.6086 (mt) cc_final: 0.5485 (mt)
REVERT: C  457 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7089 (ttp80)
REVERT: C  478 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8668 (tmtt)
REVERT: H   10 GLU cc_start: 0.7658 (mp0) cc_final: 0.7027 (mp0)
REVERT: H   38 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7687 (ttp80)
REVERT: H   62 GLN cc_start: 0.8778 (pm20) cc_final: 0.8563 (pm20)
REVERT: H   73 ASP cc_start: 0.8422 (t0) cc_final: 0.7198 (t0)
REVERT: H   74 MET cc_start: 0.7483 (mmt) cc_final: 0.7097 (mmt)
REVERT: H   80 TYR cc_start: 0.6630 (m-80) cc_final: 0.6220 (m-80)
REVERT: H   93 MET cc_start: 0.8286 (tpp) cc_final: 0.7968 (tpp)
REVERT: H  176 PHE cc_start: 0.6792 (t80) cc_final: 0.6347 (t80)
REVERT: L   13 LEU cc_start: 0.8564 (tp) cc_final: 0.7622 (tp)
REVERT: L   17 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6766 (mt-10)
REVERT: L   37 TYR cc_start: 0.7781 (m-10) cc_final: 0.7408 (m-80)
REVERT: L  134 VAL cc_start: 0.8318 (t) cc_final: 0.7917 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2040
  time to fit residues: 36.7789
Evaluate side-chains
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0970
   chunk 61 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0370
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0970
   overall best weight:    0.3254

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 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 = 0.4414 r_free = 0.4414 target = 0.175424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.140924 restraints weight = 10857.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.147196 restraints weight = 6806.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.151811 restraints weight = 4650.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6521
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5232  Z= 0.212
  Angle     :  0.700   8.722   7117  Z= 0.359
  Chirality :  0.048   0.216    797
  Planarity :  0.005   0.056    912
  Dihedral  :  9.543 104.812    796
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.71 (0.33), residues: 646
  helix: -2.34 (0.84), residues: 28
  sheet:  0.12 (0.38), residues: 219
  loop : -1.87 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 113 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.012   0.002   PHE L 141 
 TYR   0.019   0.001   TYR L  50 
 ARG   0.004   0.001   ARG L  55 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.569 
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: C  378 LYS cc_start: 0.8937 (tmmt) cc_final: 0.8627 (tmmt)
REVERT: C  392 PHE cc_start: 0.6983 (m-10) cc_final: 0.6646 (m-10)
REVERT: C  418 ILE cc_start: 0.8537 (pt) cc_final: 0.8279 (pt)
REVERT: C  422 ASN cc_start: 0.7633 (m110) cc_final: 0.7376 (m110)
REVERT: C  429 PHE cc_start: 0.8165 (t80) cc_final: 0.7487 (t80)
REVERT: C  451 TYR cc_start: 0.6074 (m-80) cc_final: 0.5597 (m-80)
REVERT: C  455 LEU cc_start: 0.6389 (mt) cc_final: 0.5842 (mt)
REVERT: C  478 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8673 (tmtt)
REVERT: H   10 GLU cc_start: 0.7673 (mp0) cc_final: 0.7072 (mp0)
REVERT: H   38 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7777 (tmm-80)
REVERT: H   47 TRP cc_start: 0.7990 (t60) cc_final: 0.6753 (t60)
REVERT: H   62 GLN cc_start: 0.8831 (pm20) cc_final: 0.8341 (pm20)
REVERT: H   73 ASP cc_start: 0.8449 (t0) cc_final: 0.7196 (t0)
REVERT: H   74 MET cc_start: 0.7506 (mmt) cc_final: 0.7140 (mmt)
REVERT: H   76 THR cc_start: 0.8209 (t) cc_final: 0.7961 (t)
REVERT: H   80 TYR cc_start: 0.6616 (m-80) cc_final: 0.6288 (m-80)
REVERT: H   93 MET cc_start: 0.8395 (tpp) cc_final: 0.8147 (tpp)
REVERT: H  176 PHE cc_start: 0.6879 (t80) cc_final: 0.6477 (t80)
REVERT: L   13 LEU cc_start: 0.8613 (tp) cc_final: 0.7624 (tp)
REVERT: L   17 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6745 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1931
  time to fit residues: 33.4547
Evaluate side-chains
  132 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0050
   chunk 42 optimal weight:    0.1980
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 45 optimal weight:    7.9990
   chunk 4 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.2394

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.4430 r_free = 0.4430 target = 0.177069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.142126 restraints weight = 10966.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.148574 restraints weight = 6791.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.153261 restraints weight = 4610.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5232  Z= 0.194
  Angle     :  0.731  12.706   7117  Z= 0.370
  Chirality :  0.048   0.219    797
  Planarity :  0.005   0.056    912
  Dihedral  :  9.475 104.113    796
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 18.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.66 (0.34), residues: 646
  helix: -2.29 (0.84), residues: 28
  sheet:  0.11 (0.37), residues: 219
  loop : -1.81 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L 150 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.026   0.002   PHE C 515 
 TYR   0.017   0.001   TYR L  50 
 ARG   0.003   0.000   ARG H  38 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.580 
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: C  354 ASN cc_start: 0.7776 (m110) cc_final: 0.7569 (m110)
REVERT: C  378 LYS cc_start: 0.8915 (tmmt) cc_final: 0.8488 (tmmt)
REVERT: C  392 PHE cc_start: 0.6975 (m-10) cc_final: 0.6662 (m-10)
REVERT: C  418 ILE cc_start: 0.8538 (pt) cc_final: 0.8287 (pt)
REVERT: C  422 ASN cc_start: 0.7684 (m110) cc_final: 0.7381 (m110)
REVERT: C  429 PHE cc_start: 0.8144 (t80) cc_final: 0.7536 (t80)
REVERT: C  451 TYR cc_start: 0.6052 (m-80) cc_final: 0.5614 (m-80)
REVERT: C  455 LEU cc_start: 0.6348 (mt) cc_final: 0.5755 (mt)
REVERT: C  462 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8847 (ttpp)
REVERT: C  478 LYS cc_start: 0.8956 (tmtt) cc_final: 0.8687 (tmtt)
REVERT: H   10 GLU cc_start: 0.7633 (mp0) cc_final: 0.6806 (mp0)
REVERT: H   62 GLN cc_start: 0.8863 (pm20) cc_final: 0.8347 (pm20)
REVERT: H   73 ASP cc_start: 0.8428 (t0) cc_final: 0.7256 (t0)
REVERT: H   76 THR cc_start: 0.8189 (t) cc_final: 0.7960 (t)
REVERT: H   80 TYR cc_start: 0.6536 (m-80) cc_final: 0.6230 (m-80)
REVERT: H   93 MET cc_start: 0.8416 (tpp) cc_final: 0.8161 (tpp)
REVERT: H   94 TYR cc_start: 0.7737 (m-10) cc_final: 0.7496 (m-10)
REVERT: H  176 PHE cc_start: 0.6885 (t80) cc_final: 0.6474 (t80)
REVERT: L   13 LEU cc_start: 0.8561 (tp) cc_final: 0.7555 (tp)
REVERT: L   17 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6667 (mt-10)
REVERT: L  134 VAL cc_start: 0.8334 (t) cc_final: 0.7936 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2029
  time to fit residues: 35.5959
Evaluate side-chains
  134 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 34 optimal weight:    0.0070
   chunk 13 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.1876

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 149 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 = 0.4449 r_free = 0.4449 target = 0.178479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.144061 restraints weight = 10843.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.150491 restraints weight = 6766.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.155088 restraints weight = 4590.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5232  Z= 0.186
  Angle     :  0.708   9.537   7117  Z= 0.360
  Chirality :  0.048   0.216    797
  Planarity :  0.005   0.056    912
  Dihedral  :  9.360 103.280    796
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.64 (0.34), residues: 646
  helix: -2.59 (0.76), residues: 34
  sheet:  0.07 (0.37), residues: 227
  loop : -1.75 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 113 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.014   0.001   PHE L 141 
 TYR   0.016   0.001   TYR L  50 
 ARG   0.006   0.001   ARG C 355 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.525 
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: C  355 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7934 (mmm160)
REVERT: C  378 LYS cc_start: 0.8916 (tmmt) cc_final: 0.8485 (tmmt)
REVERT: C  392 PHE cc_start: 0.7016 (m-10) cc_final: 0.6691 (m-10)
REVERT: C  418 ILE cc_start: 0.8545 (pt) cc_final: 0.8236 (pt)
REVERT: C  422 ASN cc_start: 0.7637 (m110) cc_final: 0.7377 (m110)
REVERT: C  429 PHE cc_start: 0.8139 (t80) cc_final: 0.7505 (t80)
REVERT: C  451 TYR cc_start: 0.5925 (m-80) cc_final: 0.5566 (m-80)
REVERT: C  455 LEU cc_start: 0.6450 (mt) cc_final: 0.5844 (mt)
REVERT: C  462 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8803 (ttpp)
REVERT: C  478 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8674 (tmtt)
REVERT: H   10 GLU cc_start: 0.7638 (mp0) cc_final: 0.6856 (mp0)
REVERT: H   38 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7738 (ttp80)
REVERT: H   62 GLN cc_start: 0.8831 (pm20) cc_final: 0.8287 (pm20)
REVERT: H   73 ASP cc_start: 0.8370 (t0) cc_final: 0.7114 (t0)
REVERT: H   74 MET cc_start: 0.7412 (mmt) cc_final: 0.7061 (mmt)
REVERT: H   76 THR cc_start: 0.8182 (t) cc_final: 0.7934 (t)
REVERT: H   80 TYR cc_start: 0.6426 (m-80) cc_final: 0.6198 (m-80)
REVERT: H  176 PHE cc_start: 0.6877 (t80) cc_final: 0.6518 (t80)
REVERT: L   13 LEU cc_start: 0.8510 (tp) cc_final: 0.7480 (tp)
REVERT: L   17 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6539 (mt-10)
REVERT: L  134 VAL cc_start: 0.8228 (t) cc_final: 0.7888 (p)
REVERT: L  174 THR cc_start: 0.7208 (m) cc_final: 0.6907 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2015
  time to fit residues: 34.5558
Evaluate side-chains
  132 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 37 optimal weight:    0.2980
   chunk 38 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0870
   chunk 39 optimal weight:    0.0970
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.1956

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L   6 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 = 0.4448 r_free = 0.4448 target = 0.178306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.143883 restraints weight = 11148.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.150331 restraints weight = 6929.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.155064 restraints weight = 4701.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6449
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5232  Z= 0.199
  Angle     :  0.721   9.005   7117  Z= 0.366
  Chirality :  0.048   0.214    797
  Planarity :  0.005   0.056    912
  Dihedral  :  9.335 103.014    796
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.65 (0.33), residues: 646
  helix: -2.67 (0.76), residues: 34
  sheet: -0.02 (0.37), residues: 220
  loop : -1.66 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 113 
 HIS   0.008   0.002   HIS L  91 
 PHE   0.016   0.002   PHE L 211 
 TYR   0.015   0.001   TYR L  50 
 ARG   0.006   0.001   ARG C 355 

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

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

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1292 Ramachandran restraints generated.
    646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  346 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7558 (mtp-110)
REVERT: C  355 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7897 (mmm160)
REVERT: C  378 LYS cc_start: 0.8910 (tmmt) cc_final: 0.8496 (tmmt)
REVERT: C  392 PHE cc_start: 0.6981 (m-10) cc_final: 0.6686 (m-10)
REVERT: C  418 ILE cc_start: 0.8574 (pt) cc_final: 0.8240 (pt)
REVERT: C  422 ASN cc_start: 0.7639 (m110) cc_final: 0.7393 (m110)
REVERT: C  425 LEU cc_start: 0.7885 (mp) cc_final: 0.7684 (mp)
REVERT: C  429 PHE cc_start: 0.8175 (t80) cc_final: 0.7579 (t80)
REVERT: C  451 TYR cc_start: 0.5884 (m-80) cc_final: 0.5569 (m-80)
REVERT: C  455 LEU cc_start: 0.6394 (mt) cc_final: 0.5535 (mt)
REVERT: C  462 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8785 (ttpp)
REVERT: C  478 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8665 (tmtt)
REVERT: H   10 GLU cc_start: 0.7608 (mp0) cc_final: 0.6856 (mp0)
REVERT: H   38 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.7713 (ttp80)
REVERT: H   62 GLN cc_start: 0.8825 (pm20) cc_final: 0.8309 (pm20)
REVERT: H   73 ASP cc_start: 0.8315 (t0) cc_final: 0.7024 (t0)
REVERT: H   74 MET cc_start: 0.7312 (mmt) cc_final: 0.6943 (mmt)
REVERT: H   76 THR cc_start: 0.8170 (t) cc_final: 0.7933 (t)
REVERT: H   93 MET cc_start: 0.8189 (tpp) cc_final: 0.7763 (tpp)
REVERT: H   94 TYR cc_start: 0.7655 (m-10) cc_final: 0.7450 (m-10)
REVERT: H  176 PHE cc_start: 0.6884 (t80) cc_final: 0.6498 (t80)
REVERT: L   13 LEU cc_start: 0.8499 (tp) cc_final: 0.7489 (tp)
REVERT: L   17 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6468 (mt-10)
REVERT: L  134 VAL cc_start: 0.8181 (t) cc_final: 0.7820 (p)
REVERT: L  174 THR cc_start: 0.7199 (m) cc_final: 0.6888 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1993
  time to fit residues: 33.1540
Evaluate side-chains
  131 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:   50.0000
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN
** L 200 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.170850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.136495 restraints weight = 11266.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.142905 restraints weight = 6970.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.147586 restraints weight = 4727.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5232  Z= 0.320
  Angle     :  0.778   8.784   7117  Z= 0.404
  Chirality :  0.050   0.216    797
  Planarity :  0.006   0.056    912
  Dihedral  :  9.747 106.083    796
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 27.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -1.81 (0.33), residues: 646
  helix: -2.63 (0.75), residues: 34
  sheet:  0.03 (0.37), residues: 217
  loop : -1.88 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP C 353 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.016   0.002   PHE L 141 
 TYR   0.026   0.002   TYR L 188 
 ARG   0.011   0.001   ARG C 493 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.44 seconds
wall clock time: 44 minutes 50.82 seconds (2690.82 seconds total)