Starting phenix.real_space_refine
on Thu Mar  6 07:09:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c89_16473/03_2025/8c89_16473_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c89_16473/03_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_16473/03_2025/8c89_16473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c89_16473/03_2025/8c89_16473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c89_16473/03_2025/8c89_16473_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c89_16473/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.12, per 1000 atoms: 1.00
  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: 1.19
  Conformation dependent library (CDL) restraints added in 576.1 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: 0.60
  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: 1.38

  Time building geometry restraints manager: 1.44 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:             8.380
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.090
  Find NCS groups from input model:        0.080
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.630
-------------------------------------------------------------------------------
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  : 0.578 
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: 0.2041
  time to fit residues: 36.6355
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  : 0.575 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.143922 restraints weight = 10923.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.150562 restraints weight = 6790.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.155275 restraints weight = 4630.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
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  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7414 (mmm160)
REVERT: C  357 ARG cc_start: 0.7259 (tpt90) cc_final: 0.6894 (tpt90)
REVERT: C  358 ILE cc_start: 0.7155 (mp) cc_final: 0.6941 (mp)
REVERT: C  392 PHE cc_start: 0.6859 (m-10) cc_final: 0.6558 (m-10)
REVERT: C  398 ASP cc_start: 0.6239 (p0) cc_final: 0.5456 (p0)
REVERT: C  418 ILE cc_start: 0.8656 (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: 0.8061 (t80) cc_final: 0.7590 (t80)
REVERT: C  451 TYR cc_start: 0.6306 (m-80) cc_final: 0.5778 (m-80)
REVERT: C  478 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8536 (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: 0.8662 (pm20) cc_final: 0.8258 (pm20)
REVERT: H   64 PHE cc_start: 0.8431 (m-10) cc_final: 0.8164 (m-10)
REVERT: H   73 ASP cc_start: 0.8563 (t0) cc_final: 0.7572 (t0)
REVERT: H   80 TYR cc_start: 0.6676 (m-80) cc_final: 0.6099 (m-80)
REVERT: H   93 MET cc_start: 0.8362 (tpp) cc_final: 0.8126 (tpp)
REVERT: H   94 TYR cc_start: 0.7732 (m-10) cc_final: 0.7465 (m-10)
REVERT: H  187 SER cc_start: 0.8137 (p) cc_final: 0.7817 (t)
REVERT: L   13 LEU cc_start: 0.8489 (tp) cc_final: 0.8206 (tp)
REVERT: L   86 MET cc_start: 0.6685 (tpp) cc_final: 0.6122 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1988
  time to fit residues: 33.6295
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  : 0.549 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.175368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.140221 restraints weight = 11158.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.146643 restraints weight = 6942.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.151242 restraints weight = 4723.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5232  Z= 0.311
  Angle     :  0.740   8.551   7117  Z= 0.388
  Chirality :  0.049   0.231    797
  Planarity :  0.006   0.051    912
  Dihedral  : 10.695 112.348    796
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 25.05
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.46 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.49 %
    Favored  : 94.34 %
  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: -2.06 (0.33), residues: 646
  helix: -2.38 (0.80), residues: 28
  sheet: -0.20 (0.36), residues: 214
  loop : -2.07 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 353 
 HIS   0.005   0.002   HIS L 191 
 PHE   0.014   0.002   PHE H 110 
 TYR   0.021   0.002   TYR C 380 
 ARG   0.008   0.001   ARG C 457 

*********************** 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
  149 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  355 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7616 (mmm160)
REVERT: C  357 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7067 (tpt90)
REVERT: C  378 LYS cc_start: 0.8923 (tmmt) cc_final: 0.8651 (tmmt)
REVERT: C  392 PHE cc_start: 0.6977 (m-10) cc_final: 0.6594 (m-10)
REVERT: C  398 ASP cc_start: 0.6474 (p0) cc_final: 0.5102 (p0)
REVERT: C  418 ILE cc_start: 0.8730 (pt) cc_final: 0.8427 (pt)
REVERT: C  423 TYR cc_start: 0.7890 (t80) cc_final: 0.7411 (t80)
REVERT: C  425 LEU cc_start: 0.8192 (mp) cc_final: 0.7940 (mp)
REVERT: C  429 PHE cc_start: 0.8141 (t80) cc_final: 0.7567 (t80)
REVERT: C  451 TYR cc_start: 0.6118 (m-80) cc_final: 0.5725 (m-80)
REVERT: C  457 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7377 (ttp80)
REVERT: C  478 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8545 (tmtt)
REVERT: H   10 GLU cc_start: 0.7850 (mp0) cc_final: 0.7456 (mp0)
REVERT: H   38 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7706 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8714 (pm20) cc_final: 0.8227 (pm20)
REVERT: H   64 PHE cc_start: 0.8524 (m-10) cc_final: 0.8210 (m-10)
REVERT: H   73 ASP cc_start: 0.8622 (t0) cc_final: 0.7507 (t0)
REVERT: H   80 TYR cc_start: 0.6734 (m-80) cc_final: 0.6157 (m-80)
REVERT: H   93 MET cc_start: 0.8452 (tpp) cc_final: 0.8251 (tpp)
REVERT: H   94 TYR cc_start: 0.7780 (m-10) cc_final: 0.7523 (m-10)
REVERT: L   13 LEU cc_start: 0.8672 (tp) cc_final: 0.8304 (tp)
REVERT: L  142 TYR cc_start: 0.7314 (t80) cc_final: 0.7078 (t80)
REVERT: L  174 THR cc_start: 0.7089 (m) cc_final: 0.6722 (t)
REVERT: L  201 GLN cc_start: 0.8424 (mp10) cc_final: 0.8076 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2075
  time to fit residues: 38.4523
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  : 0.531 
-------------------------------------------------------------------------------
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:    0.0060
   chunk 25 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0270
   chunk 47 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0970
   chunk 50 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.1052

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
C 505 HIS
** H  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   6 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 = 0.4488 r_free = 0.4488 target = 0.181501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.145914 restraints weight = 11213.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.152352 restraints weight = 7020.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.157317 restraints weight = 4803.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5232  Z= 0.172
  Angle     :  0.700   8.846   7117  Z= 0.355
  Chirality :  0.048   0.227    797
  Planarity :  0.005   0.054    912
  Dihedral  :  9.762 104.805    796
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.20 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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: -1.85 (0.33), residues: 646
  helix: -2.32 (0.85), residues: 28
  sheet: -0.02 (0.37), residues: 220
  loop : -1.96 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.005   0.002   HIS C 519 
 PHE   0.011   0.002   PHE C 392 
 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  : 0.556 
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: 0.8064 (mmm160) cc_final: 0.7620 (mmm160)
REVERT: C  392 PHE cc_start: 0.6991 (m-10) cc_final: 0.6637 (m-10)
REVERT: C  398 ASP cc_start: 0.6127 (p0) cc_final: 0.5053 (p0)
REVERT: C  418 ILE cc_start: 0.8601 (pt) cc_final: 0.8374 (pt)
REVERT: C  425 LEU cc_start: 0.8142 (mp) cc_final: 0.7861 (mp)
REVERT: C  429 PHE cc_start: 0.8067 (t80) cc_final: 0.7665 (t80)
REVERT: C  451 TYR cc_start: 0.6042 (m-80) cc_final: 0.5623 (m-80)
REVERT: H   10 GLU cc_start: 0.7733 (mp0) cc_final: 0.7249 (mp0)
REVERT: H   38 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7759 (tmm-80)
REVERT: H   62 GLN cc_start: 0.8662 (pm20) cc_final: 0.8347 (pm20)
REVERT: H   64 PHE cc_start: 0.8481 (m-10) cc_final: 0.8217 (m-10)
REVERT: H   73 ASP cc_start: 0.8372 (t0) cc_final: 0.7290 (t0)
REVERT: H   80 TYR cc_start: 0.6590 (m-80) cc_final: 0.6138 (m-80)
REVERT: L   13 LEU cc_start: 0.8488 (tp) cc_final: 0.8165 (tp)
REVERT: L  174 THR cc_start: 0.6723 (m) cc_final: 0.6430 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2211
  time to fit residues: 38.8313
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  : 0.585 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0010
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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**
L  32 ASN
L  38 GLN
L 126 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.175670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.140571 restraints weight = 11239.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.147077 restraints weight = 6971.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.151799 restraints weight = 4723.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5232  Z= 0.269
  Angle     :  0.725   9.061   7117  Z= 0.374
  Chirality :  0.048   0.226    797
  Planarity :  0.006   0.053    912
  Dihedral  :  9.777 104.905    796
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 22.27
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 11.15 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  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: -1.79 (0.33), residues: 646
  helix: -2.29 (0.86), residues: 28
  sheet:  0.12 (0.38), residues: 208
  loop : -1.93 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 353 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.013   0.002   PHE L 100 
 TYR   0.028   0.002   TYR L 188 
 ARG   0.008   0.001   ARG C 493 

*********************** 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
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.583 
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: 0.7748 (m110) cc_final: 0.7545 (m110)
REVERT: C  392 PHE cc_start: 0.6985 (m-10) cc_final: 0.6603 (m-10)
REVERT: C  418 ILE cc_start: 0.8639 (pt) cc_final: 0.8360 (pt)
REVERT: C  429 PHE cc_start: 0.8108 (t80) cc_final: 0.7583 (t80)
REVERT: C  451 TYR cc_start: 0.6035 (m-80) cc_final: 0.5611 (m-80)
REVERT: C  457 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7331 (ttp80)
REVERT: C  462 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8858 (ttpp)
REVERT: C  478 LYS cc_start: 0.8942 (tmtt) cc_final: 0.8645 (tmtt)
REVERT: H   10 GLU cc_start: 0.7805 (mp0) cc_final: 0.7319 (mp0)
REVERT: H   38 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7796 (tmm-80)
REVERT: H   64 PHE cc_start: 0.8545 (m-10) cc_final: 0.8240 (m-10)
REVERT: H   73 ASP cc_start: 0.8509 (t0) cc_final: 0.7425 (t0)
REVERT: H   76 THR cc_start: 0.8156 (t) cc_final: 0.7940 (t)
REVERT: H   80 TYR cc_start: 0.6539 (m-80) cc_final: 0.6146 (m-80)
REVERT: H   94 TYR cc_start: 0.7772 (m-10) cc_final: 0.7513 (m-10)
REVERT: H  176 PHE cc_start: 0.6742 (t80) cc_final: 0.6478 (t80)
REVERT: L   13 LEU cc_start: 0.8591 (tp) cc_final: 0.8206 (tp)
REVERT: L   37 TYR cc_start: 0.7654 (m-10) cc_final: 0.7330 (m-80)
REVERT: L  134 VAL cc_start: 0.8277 (t) cc_final: 0.7846 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2176
  time to fit residues: 37.7455
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  : 0.508 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 30 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0970
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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
L  32 ASN
L 126 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.174798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.140177 restraints weight = 10996.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.146557 restraints weight = 6823.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.151009 restraints weight = 4626.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5232  Z= 0.255
  Angle     :  0.732   8.850   7117  Z= 0.377
  Chirality :  0.049   0.226    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.681 104.089    796
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 21.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  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: -1.82 (0.33), residues: 646
  helix: -2.37 (0.84), residues: 28
  sheet: -0.14 (0.37), residues: 226
  loop : -1.86 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L 150 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.014   0.002   PHE C 429 
 TYR   0.021   0.002   TYR L 188 
 ARG   0.004   0.001   ARG L  55 

*********************** 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
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7801 (m110) cc_final: 0.7581 (m110)
REVERT: C  392 PHE cc_start: 0.6999 (m-10) cc_final: 0.6644 (m-10)
REVERT: C  418 ILE cc_start: 0.8624 (pt) cc_final: 0.8396 (pt)
REVERT: C  429 PHE cc_start: 0.8052 (t80) cc_final: 0.7514 (t80)
REVERT: C  451 TYR cc_start: 0.6148 (m-80) cc_final: 0.5677 (m-80)
REVERT: C  455 LEU cc_start: 0.6027 (mt) cc_final: 0.5395 (mt)
REVERT: C  462 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8805 (ttpp)
REVERT: C  464 PHE cc_start: 0.8967 (m-80) cc_final: 0.8690 (m-10)
REVERT: C  478 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8574 (tmtt)
REVERT: C  513 LEU cc_start: 0.7731 (mt) cc_final: 0.7526 (mt)
REVERT: H   10 GLU cc_start: 0.7768 (mp0) cc_final: 0.7233 (mp0)
REVERT: H   38 ARG cc_start: 0.8111 (ttp80) cc_final: 0.7870 (tmm-80)
REVERT: H   47 TRP cc_start: 0.8057 (t60) cc_final: 0.6632 (t60)
REVERT: H   62 GLN cc_start: 0.8748 (pm20) cc_final: 0.8169 (pm20)
REVERT: H   73 ASP cc_start: 0.8519 (t0) cc_final: 0.7349 (t0)
REVERT: H   76 THR cc_start: 0.8202 (t) cc_final: 0.7987 (t)
REVERT: H   80 TYR cc_start: 0.6497 (m-80) cc_final: 0.6143 (m-80)
REVERT: H   94 TYR cc_start: 0.7916 (m-10) cc_final: 0.7597 (m-10)
REVERT: H  176 PHE cc_start: 0.6804 (t80) cc_final: 0.6480 (t80)
REVERT: L   13 LEU cc_start: 0.8621 (tp) cc_final: 0.7642 (tp)
REVERT: L   17 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6866 (mt-10)
REVERT: L   37 TYR cc_start: 0.7719 (m-10) cc_final: 0.7425 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2009
  time to fit residues: 35.0418
Evaluate side-chains
  135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0770
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.4138

-------------------------------------------------------------------------------
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  32 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 126 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.174417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.140592 restraints weight = 10917.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.146862 restraints weight = 6796.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.151322 restraints weight = 4608.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5232  Z= 0.243
  Angle     :  0.736   9.605   7117  Z= 0.377
  Chirality :  0.049   0.217    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.680 105.031    796
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.37 %
    Favored  : 89.47 %
  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: -1.74 (0.34), residues: 646
  helix: -2.37 (0.81), residues: 28
  sheet:  0.08 (0.38), residues: 219
  loop : -1.89 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 113 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.031   0.002   PHE C 515 
 TYR   0.020   0.002   TYR L  50 
 ARG   0.006   0.001   ARG C 493 

*********************** 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
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7779 (m110) cc_final: 0.7570 (m110)
REVERT: C  378 LYS cc_start: 0.8962 (tmmt) cc_final: 0.8661 (tmmt)
REVERT: C  392 PHE cc_start: 0.6976 (m-10) cc_final: 0.6603 (m-10)
REVERT: C  418 ILE cc_start: 0.8596 (pt) cc_final: 0.8294 (pt)
REVERT: C  422 ASN cc_start: 0.7568 (m110) cc_final: 0.7250 (m110)
REVERT: C  451 TYR cc_start: 0.6144 (m-80) cc_final: 0.5687 (m-80)
REVERT: C  453 TYR cc_start: 0.7447 (p90) cc_final: 0.7127 (p90)
REVERT: C  462 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8797 (ttpp)
REVERT: C  478 LYS cc_start: 0.8938 (tmtt) cc_final: 0.8583 (tmtt)
REVERT: H   10 GLU cc_start: 0.7722 (mp0) cc_final: 0.7160 (mp0)
REVERT: H   62 GLN cc_start: 0.8778 (pm20) cc_final: 0.8182 (pm20)
REVERT: H   73 ASP cc_start: 0.8480 (t0) cc_final: 0.7204 (t0)
REVERT: H   74 MET cc_start: 0.7491 (mmt) cc_final: 0.7146 (mmt)
REVERT: H   76 THR cc_start: 0.8198 (t) cc_final: 0.7973 (t)
REVERT: H   80 TYR cc_start: 0.6534 (m-80) cc_final: 0.6149 (m-80)
REVERT: H   94 TYR cc_start: 0.7778 (m-10) cc_final: 0.7464 (m-10)
REVERT: H  176 PHE cc_start: 0.6827 (t80) cc_final: 0.6490 (t80)
REVERT: L   13 LEU cc_start: 0.8641 (tp) cc_final: 0.7676 (tp)
REVERT: L   17 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6822 (mt-10)
REVERT: L   37 TYR cc_start: 0.7772 (m-10) cc_final: 0.7434 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1935
  time to fit residues: 34.5823
Evaluate side-chains
  135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 1 optimal weight:    0.0000
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0970
   chunk 45 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.3982

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 200 HIS ** 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 = 0.4411 r_free = 0.4411 target = 0.175226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.140608 restraints weight = 10881.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.147061 restraints weight = 6765.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.151632 restraints weight = 4590.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5232  Z= 0.242
  Angle     :  0.733   8.825   7117  Z= 0.378
  Chirality :  0.050   0.220    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.604 104.506    796
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 10.37 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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: -1.74 (0.34), residues: 646
  helix: -2.38 (0.86), residues: 28
  sheet:  0.09 (0.38), residues: 219
  loop : -1.89 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H  47 
 HIS   0.003   0.001   HIS L 191 
 PHE   0.014   0.002   PHE C 456 
 TYR   0.019   0.002   TYR L  50 
 ARG   0.004   0.001   ARG C 355 

*********************** 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
  143 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7769 (m110) cc_final: 0.7509 (m110)
REVERT: C  355 ARG cc_start: 0.8345 (mmm160) cc_final: 0.8037 (mmm160)
REVERT: C  377 PHE cc_start: 0.8664 (t80) cc_final: 0.8344 (t80)
REVERT: C  392 PHE cc_start: 0.6952 (m-10) cc_final: 0.6662 (m-10)
REVERT: C  418 ILE cc_start: 0.8631 (pt) cc_final: 0.8321 (pt)
REVERT: C  422 ASN cc_start: 0.7544 (m110) cc_final: 0.7231 (m110)
REVERT: C  425 LEU cc_start: 0.8160 (tp) cc_final: 0.7916 (tp)
REVERT: C  451 TYR cc_start: 0.6088 (m-80) cc_final: 0.5664 (m-80)
REVERT: C  462 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8777 (ttpp)
REVERT: H   10 GLU cc_start: 0.7692 (mp0) cc_final: 0.7093 (mp0)
REVERT: H   47 TRP cc_start: 0.7999 (t60) cc_final: 0.7086 (t60)
REVERT: H   62 GLN cc_start: 0.8780 (pm20) cc_final: 0.8201 (pm20)
REVERT: H   73 ASP cc_start: 0.8452 (t0) cc_final: 0.7164 (t0)
REVERT: H   74 MET cc_start: 0.7461 (mmt) cc_final: 0.7142 (mmt)
REVERT: H   76 THR cc_start: 0.8211 (t) cc_final: 0.7968 (t)
REVERT: H   80 TYR cc_start: 0.6570 (m-80) cc_final: 0.6269 (m-80)
REVERT: H  176 PHE cc_start: 0.6902 (t80) cc_final: 0.6506 (t80)
REVERT: L   13 LEU cc_start: 0.8678 (tp) cc_final: 0.7703 (tp)
REVERT: L   17 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6757 (mt-10)
REVERT: L   37 TYR cc_start: 0.7776 (m-10) cc_final: 0.7403 (m-80)
REVERT: L  134 VAL cc_start: 0.8328 (t) cc_final: 0.7999 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1771
  time to fit residues: 32.3664
Evaluate side-chains
  135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 13 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0370
   chunk 53 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.3258

-------------------------------------------------------------------------------
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
L  32 ASN
** 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 = 0.4415 r_free = 0.4415 target = 0.175692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.141530 restraints weight = 10780.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147848 restraints weight = 6717.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.152394 restraints weight = 4553.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5232  Z= 0.224
  Angle     :  0.745   8.817   7117  Z= 0.385
  Chirality :  0.049   0.218    797
  Planarity :  0.006   0.076    912
  Dihedral  :  9.553 104.229    796
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 21.57
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.91 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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 (0.34), residues: 646
  helix: -2.38 (0.86), residues: 28
  sheet:  0.05 (0.37), residues: 222
  loop : -1.84 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 113 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.026   0.002   PHE C 515 
 TYR   0.019   0.001   TYR L  50 
 ARG   0.007   0.001   ARG H  38 

*********************** 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
  139 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  354 ASN cc_start: 0.7773 (m110) cc_final: 0.7528 (m110)
REVERT: C  377 PHE cc_start: 0.8676 (t80) cc_final: 0.8320 (t80)
REVERT: C  392 PHE cc_start: 0.6942 (m-10) cc_final: 0.6647 (m-10)
REVERT: C  418 ILE cc_start: 0.8636 (pt) cc_final: 0.8363 (pt)
REVERT: C  422 ASN cc_start: 0.7504 (m110) cc_final: 0.7224 (m110)
REVERT: C  436 TRP cc_start: 0.9079 (p90) cc_final: 0.7678 (p90)
REVERT: C  451 TYR cc_start: 0.6196 (m-80) cc_final: 0.5784 (m-80)
REVERT: C  462 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8764 (ttpp)
REVERT: H   10 GLU cc_start: 0.7680 (mp0) cc_final: 0.6871 (mp0)
REVERT: H   47 TRP cc_start: 0.8091 (t60) cc_final: 0.7126 (t60)
REVERT: H   62 GLN cc_start: 0.8795 (pm20) cc_final: 0.8467 (pm20)
REVERT: H   73 ASP cc_start: 0.8420 (t0) cc_final: 0.7117 (t0)
REVERT: H   74 MET cc_start: 0.7461 (mmt) cc_final: 0.7108 (mmt)
REVERT: H   76 THR cc_start: 0.8213 (t) cc_final: 0.7988 (t)
REVERT: H   80 TYR cc_start: 0.6496 (m-80) cc_final: 0.6221 (m-80)
REVERT: H   94 TYR cc_start: 0.7739 (m-10) cc_final: 0.7389 (m-10)
REVERT: L   13 LEU cc_start: 0.8620 (tp) cc_final: 0.7591 (tp)
REVERT: L   17 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6677 (mt-10)
REVERT: L   37 TYR cc_start: 0.7733 (m-10) cc_final: 0.7440 (m-80)
REVERT: L   92 TYR cc_start: 0.8114 (p90) cc_final: 0.7542 (p90)
REVERT: L  134 VAL cc_start: 0.8269 (t) cc_final: 0.8012 (p)
REVERT: L  174 THR cc_start: 0.7233 (m) cc_final: 0.6976 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1859
  time to fit residues: 32.4781
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  : 0.432 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.3980
   chunk 38 optimal weight:    0.0030
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0980
   chunk 39 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 20 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.1228

-------------------------------------------------------------------------------
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  32 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4460 r_free = 0.4460 target = 0.179116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.145786 restraints weight = 11089.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.152279 restraints weight = 6819.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.156958 restraints weight = 4590.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5232  Z= 0.182
  Angle     :  0.721   8.964   7117  Z= 0.370
  Chirality :  0.049   0.214    797
  Planarity :  0.006   0.061    912
  Dihedral  :  9.338 102.380    796
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.74 %
    Favored  : 92.11 %
  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: -1.62 (0.34), residues: 646
  helix: -2.37 (0.85), residues: 28
  sheet:  0.18 (0.37), residues: 222
  loop : -1.82 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 113 
 HIS   0.005   0.001   HIS C 519 
 PHE   0.014   0.002   PHE L 141 
 TYR   0.022   0.001   TYR L  50 
 ARG   0.008   0.001   ARG H  38 

********************** 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
  140 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.501 
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: 0.7718 (mtp-110) cc_final: 0.7514 (mtp-110)
REVERT: C  354 ASN cc_start: 0.7665 (m110) cc_final: 0.7432 (m110)
REVERT: C  378 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8455 (tmmt)
REVERT: C  392 PHE cc_start: 0.6975 (m-10) cc_final: 0.6677 (m-10)
REVERT: C  418 ILE cc_start: 0.8613 (pt) cc_final: 0.8316 (pt)
REVERT: C  422 ASN cc_start: 0.7497 (m110) cc_final: 0.7247 (m110)
REVERT: C  429 PHE cc_start: 0.7776 (t80) cc_final: 0.7567 (t80)
REVERT: C  451 TYR cc_start: 0.5958 (m-80) cc_final: 0.5600 (m-80)
REVERT: C  455 LEU cc_start: 0.5885 (mt) cc_final: 0.5251 (mt)
REVERT: C  462 LYS cc_start: 0.9051 (ttpp) cc_final: 0.8711 (ttpp)
REVERT: H   10 GLU cc_start: 0.7640 (mp0) cc_final: 0.6889 (mp0)
REVERT: H   47 TRP cc_start: 0.7955 (t60) cc_final: 0.7030 (t60)
REVERT: H   62 GLN cc_start: 0.8773 (pm20) cc_final: 0.8277 (pm20)
REVERT: H   73 ASP cc_start: 0.8245 (t0) cc_final: 0.6925 (t0)
REVERT: H   74 MET cc_start: 0.7287 (mmt) cc_final: 0.6912 (mmt)
REVERT: H   76 THR cc_start: 0.8186 (t) cc_final: 0.7928 (t)
REVERT: H   80 TYR cc_start: 0.6337 (m-80) cc_final: 0.6128 (m-80)
REVERT: H   94 TYR cc_start: 0.7687 (m-10) cc_final: 0.6964 (m-10)
REVERT: H  176 PHE cc_start: 0.6908 (t80) cc_final: 0.6460 (t80)
REVERT: L   13 LEU cc_start: 0.8479 (tp) cc_final: 0.7468 (tp)
REVERT: L   17 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6475 (mt-10)
REVERT: L  134 VAL cc_start: 0.8213 (t) cc_final: 0.7941 (p)
REVERT: L  174 THR cc_start: 0.7052 (m) cc_final: 0.6769 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1906
  time to fit residues: 33.3129
Evaluate side-chains
  135 residues out of total 565 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0050
   chunk 32 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5594

-------------------------------------------------------------------------------
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  32 ASN
** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 212 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.138618 restraints weight = 11328.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.144862 restraints weight = 7031.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.149729 restraints weight = 4795.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.4102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5232  Z= 0.283
  Angle     :  0.765   8.921   7117  Z= 0.403
  Chirality :  0.050   0.216    797
  Planarity :  0.006   0.054    912
  Dihedral  :  9.625 104.361    796
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 25.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    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: -1.76 (0.33), residues: 646
  helix: -2.31 (0.86), residues: 28
  sheet:  0.07 (0.37), residues: 222
  loop : -1.93 (0.31), residues: 396

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   0.015   0.002   PHE L 141 
 TYR   0.022   0.002   TYR L  50 
 ARG   0.009   0.001   ARG L  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2457.31 seconds
wall clock time: 43 minutes 35.83 seconds (2615.83 seconds total)