Starting phenix.real_space_refine
on Fri Aug 22 14:59:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2a_42903/08_2025/8v2a_42903.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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      22      5.16       5
     C    2846      2.51       5
     N     774      2.21       5
     O     880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4522
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1376
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 8, 'TRANS': 163}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1611
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 11, 'TRANS': 187}
    Chain: "C"
      Number of atoms: 1395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1395
          Classifications: {'peptide': 180}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 169}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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: "F"
      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: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.61, per 1000 atoms: 0.36
  Number of scatterers: 4522
  At special positions: 0
  Unit cell: (81.7, 108.36, 101.48, 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      22     16.00
     O     880      8.00
     N     774      7.00
     C    2846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 341 " - pdb=" SG  CYS C 351 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG B 701 " - " ASN B 131 "
      " NAG B 702 " - " ASN B 227 "
      " NAG B 703 " - " ASN B 157 "
      " NAG C 901 " - " ASN C 303 "
      " NAG D   1 " - " ASN A 100 "
      " NAG E   1 " - " ASN C 407 "
      " NAG F   1 " - " ASN C 426 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 199.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 10 sheets defined
      28.5% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 50
    Processing helix  chain 'A' and resid 51 through 63
      removed outlier: 4.608A  pdb=" N   ASP A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
      Proline residue:  A  58  - end of helix
    Processing helix  chain 'A' and resid 67 through 73
    Processing helix  chain 'A' and resid 83 through 90
    Processing helix  chain 'A' and resid 93 through 117
    Processing helix  chain 'A' and resid 119 through 127
    Processing helix  chain 'A' and resid 130 through 158
      Proline residue:  A 141  - end of helix
      removed outlier: 3.603A  pdb=" N   ASP A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 212
      removed outlier: 4.160A  pdb=" N   LYS A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 189 " --> pdb=" O   PHE A 185 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TRP A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 218
    Processing helix  chain 'B' and resid 247 through 252
      removed outlier: 3.539A  pdb=" N   LYS B 250 " --> pdb=" O   PRO B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 4.211A  pdb=" N   ALA B 278 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 430
      No H-bonds generated for 'chain 'C' and resid 428 through 430'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 181 through 183
      removed outlier: 3.805A  pdb=" N   CYS B 182 " --> pdb=" O   CYS B 144 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   CYS B 144 " --> pdb=" O   CYS B 182 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   LYS B 221 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL B 136 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 171
      removed outlier: 5.565A  pdb=" N   SER B 162 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ASP B 171 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B 160 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU B 201 " --> pdb=" O   ASN B 157 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLY B 205 " --> pdb=" O   ASN B 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171
      removed outlier: 5.565A  pdb=" N   SER B 162 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ASP B 171 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU B 160 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU B 201 " --> pdb=" O   ASN B 157 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE B 194 " --> pdb=" O   PHE B 214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 226 through 231
      removed outlier: 5.494A  pdb=" N   ASN B 227 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   THR B 245 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 271
    Processing sheet with id=AA6, first strand: chain 'C' and resid 254 through 255
      removed outlier: 3.528A  pdb=" N   ILE C 299 " --> pdb=" O   PHE C 269 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 262
    Processing sheet with id=AA8, first strand: chain 'C' and resid 285 through 287
      removed outlier: 3.560A  pdb=" N   CYS C 287 " --> pdb=" O   ALA C 280 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ALA C 280 " --> pdb=" O   CYS C 287 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 343
      removed outlier: 5.613A  pdb=" N   GLN C 338 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASN C 354 " --> pdb=" O   GLN C 338 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 381

    196 hydrogen bonds defined for protein.
    528 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.51

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1457
        1.34 -     1.46: 727
        1.46 -     1.57: 2404
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 4617
  Sorted by residual:
  bond pdb=" N   GLU C 386 "
       pdb=" CA  GLU C 386 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.97e+00
  bond pdb=" N   ASN C 390 "
       pdb=" CA  ASN C 390 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.23e-02 6.61e+03 6.29e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.72e+00
  bond pdb=" N   ALA C 387 "
       pdb=" CA  ALA C 387 "
    ideal  model  delta    sigma   weight residual
    1.454  1.482 -0.027 1.44e-02 4.82e+03 3.65e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.38e+00
  ... (remaining 4612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 6100
        1.64 -     3.29: 142
        3.29 -     4.93: 14
        4.93 -     6.58: 2
        6.58 -     8.22: 1
  Bond angle restraints: 6259
  Sorted by residual:
  angle pdb=" N   ASN C 313 "
        pdb=" CA  ASN C 313 "
        pdb=" C   ASN C 313 "
      ideal   model   delta    sigma   weight residual
     109.15  117.37   -8.22 1.44e+00 4.82e-01 3.26e+01
  angle pdb=" CA  THR C 389 "
        pdb=" CB  THR C 389 "
        pdb=" OG1 THR C 389 "
      ideal   model   delta    sigma   weight residual
     109.60  104.93    4.67 1.50e+00 4.44e-01 9.70e+00
  angle pdb=" C   ALA C 385 "
        pdb=" N   GLU C 386 "
        pdb=" CA  GLU C 386 "
      ideal   model   delta    sigma   weight residual
     122.99  118.73    4.26 1.41e+00 5.03e-01 9.13e+00
  angle pdb=" CA  GLU C 391 "
        pdb=" C   GLU C 391 "
        pdb=" O   GLU C 391 "
      ideal   model   delta    sigma   weight residual
     121.39  118.38    3.01 1.12e+00 7.97e-01 7.24e+00
  angle pdb=" N   THR C 389 "
        pdb=" CA  THR C 389 "
        pdb=" C   THR C 389 "
      ideal   model   delta    sigma   weight residual
     111.71  108.80    2.91 1.15e+00 7.56e-01 6.42e+00
  ... (remaining 6254 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.47: 2713
       20.47 -    40.94: 158
       40.94 -    61.41: 44
       61.41 -    81.88: 8
       81.88 -   102.34: 17
  Dihedral angle restraints: 2940
    sinusoidal: 1336
      harmonic: 1604
  Sorted by residual:
  dihedral pdb=" CB  CYS A  31 "
           pdb=" SG  CYS A  31 "
           pdb=" SG  CYS A 152 "
           pdb=" CB  CYS A 152 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.65  -55.65     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CA  PRO B 291 "
           pdb=" C   PRO B 291 "
           pdb=" N   PHE B 292 "
           pdb=" CA  PHE B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.30   24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" C1  NAG B 702 "
           pdb=" C2  NAG B 702 "
           pdb=" C3  NAG B 702 "
           pdb=" O3  NAG B 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -72.75 -102.34     1      3.00e+01 1.11e-03 1.29e+01
  ... (remaining 2937 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 610
       0.055 -    0.109: 103
       0.109 -    0.164: 15
       0.164 -    0.218: 0
       0.218 -    0.273: 1
  Chirality restraints: 729
  Sorted by residual:
  chirality pdb=" CA  ASN C 313 "
            pdb=" N   ASN C 313 "
            pdb=" C   ASN C 313 "
            pdb=" CB  ASN C 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  ILE B 272 "
            pdb=" N   ILE B 272 "
            pdb=" C   ILE B 272 "
            pdb=" CB  ILE B 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL A  67 "
            pdb=" N   VAL A  67 "
            pdb=" C   VAL A  67 "
            pdb=" CB  VAL A  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  ... (remaining 726 not shown)

  Planarity restraints: 800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 414 "   -0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO C 415 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 415 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 415 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  57 "    0.021 5.00e-02 4.00e+02   3.13e-02 1.56e+00
        pdb=" N   PRO A  58 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 385 "    0.006 2.00e-02 2.50e+03   1.11e-02 1.23e+00
        pdb=" C   ALA C 385 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ALA C 385 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLU C 386 "    0.006 2.00e-02 2.50e+03
  ... (remaining 797 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1061
        2.79 -     3.32: 4049
        3.32 -     3.85: 6884
        3.85 -     4.37: 7539
        4.37 -     4.90: 13477
  Nonbonded interactions: 33010
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 229 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NE  ARG A  36 "
            pdb=" OE2 GLU A 214 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OG1 THR C 252 "
            pdb=" OE1 GLN C 257 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" NE2 GLN C 420 "
            pdb=" O6  NAG E   2 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" O   PRO A  82 "
            pdb=" NH2 ARG A 200 "
     model   vdw
     2.385 3.120
  ... (remaining 33005 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 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
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      :  0.003   0.049   4632  Z= 0.189
  Angle     :  0.603   8.223   6299  Z= 0.330
  Chirality :  0.044   0.273    729
  Planarity :  0.004   0.044    793
  Dihedral  : 16.756 102.344   1885
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.07 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.33), residues: 543
  helix:  0.85 (0.45), residues: 127
  sheet: -1.21 (0.36), residues: 171
  loop : -2.11 (0.34), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 262 
 TYR   0.009   0.001   TYR A  35 
 PHE   0.005   0.001   PHE C 408 
 TRP   0.014   0.001   TRP A 212 
 HIS   0.002   0.000   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4617)
  covalent geometry    : angle       0.58371 ( 6259)
  SS BOND              : bond        0.00164 (    5)
  SS BOND              : angle       0.46043 (   10)
  hydrogen bonds       : bond        0.20195 (  188)
  hydrogen bonds       : angle       6.70487 (  528)
  link_BETA1-4         : bond        0.00307 (    3)
  link_BETA1-4         : angle       2.38148 (    9)
  link_NAG-ASN         : bond        0.00227 (    7)
  link_NAG-ASN         : angle       2.19373 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8728 (tpp) cc_final: 0.8419 (tpp)
REVERT: A  211 LYS cc_start: 0.7795 (tppp) cc_final: 0.7379 (ttpt)
REVERT: C  402 ASN cc_start: 0.7929 (t0) cc_final: 0.7700 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1140
  time to fit residues: 11.6621
Evaluate side-chains
  53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0770
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 108 HIS
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 GLN
B 202 ASN
B 258 ASN
B 271 GLN
C 313 ASN
C 321 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.107789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.092473 restraints weight = 11907.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.094605 restraints weight = 7457.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.096062 restraints weight = 5514.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.096927 restraints weight = 4475.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.097635 restraints weight = 3908.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4632  Z= 0.121
  Angle     :  0.616   6.473   6299  Z= 0.305
  Chirality :  0.044   0.189    729
  Planarity :  0.004   0.034    793
  Dihedral  : 13.157  77.642    805
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.58 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.35), residues: 543
  helix:  1.94 (0.46), residues: 127
  sheet: -0.62 (0.37), residues: 161
  loop : -1.55 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 381 
 TYR   0.009   0.001   TYR A  35 
 PHE   0.007   0.001   PHE C 397 
 TRP   0.011   0.001   TRP A 212 
 HIS   0.009   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4617)
  covalent geometry    : angle       0.60233 ( 6259)
  SS BOND              : bond        0.00143 (    5)
  SS BOND              : angle       0.45341 (   10)
  hydrogen bonds       : bond        0.05239 (  188)
  hydrogen bonds       : angle       5.30418 (  528)
  link_BETA1-4         : bond        0.00280 (    3)
  link_BETA1-4         : angle       2.27236 (    9)
  link_NAG-ASN         : bond        0.00157 (    7)
  link_NAG-ASN         : angle       1.88046 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8710 (tpp) cc_final: 0.8422 (tpp)
REVERT: A  211 LYS cc_start: 0.7760 (tppp) cc_final: 0.7483 (ttpt)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.0958
  time to fit residues: 7.7358
Evaluate side-chains
  55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain C residue  313 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 313 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.105211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.089780 restraints weight = 12087.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.091885 restraints weight = 7578.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.093299 restraints weight = 5557.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.094259 restraints weight = 4518.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.094848 restraints weight = 3909.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4632  Z= 0.138
  Angle     :  0.611   7.353   6299  Z= 0.299
  Chirality :  0.044   0.178    729
  Planarity :  0.004   0.031    793
  Dihedral  :  9.992  56.967    805
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.02 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.35), residues: 543
  helix:  2.34 (0.46), residues: 127
  sheet: -0.27 (0.38), residues: 162
  loop : -1.34 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 381 
 TYR   0.009   0.001   TYR B 186 
 PHE   0.008   0.001   PHE B 297 
 TRP   0.008   0.001   TRP A 212 
 HIS   0.008   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4617)
  covalent geometry    : angle       0.59498 ( 6259)
  SS BOND              : bond        0.00158 (    5)
  SS BOND              : angle       0.38661 (   10)
  hydrogen bonds       : bond        0.05302 (  188)
  hydrogen bonds       : angle       4.96856 (  528)
  link_BETA1-4         : bond        0.00296 (    3)
  link_BETA1-4         : angle       2.45705 (    9)
  link_NAG-ASN         : bond        0.00150 (    7)
  link_NAG-ASN         : angle       1.99156 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8822 (tpp) cc_final: 0.8515 (tpp)
REVERT: A  211 LYS cc_start: 0.7890 (tppp) cc_final: 0.7596 (ttpt)
REVERT: C  349 ILE cc_start: 0.7719 (mt) cc_final: 0.7450 (tt)
REVERT: C  410 LEU cc_start: 0.8851 (tp) cc_final: 0.8634 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0967
  time to fit residues: 6.9479
Evaluate side-chains
  54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.104634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.089197 restraints weight = 12131.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.091314 restraints weight = 7540.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.092755 restraints weight = 5542.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.093692 restraints weight = 4491.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.094240 restraints weight = 3895.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4632  Z= 0.130
  Angle     :  0.597   6.470   6299  Z= 0.289
  Chirality :  0.043   0.142    729
  Planarity :  0.004   0.033    793
  Dihedral  :  7.259  56.125    805
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.43 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.36), residues: 543
  helix:  2.44 (0.46), residues: 128
  sheet: -0.18 (0.38), residues: 168
  loop : -1.11 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  54 
 TYR   0.008   0.001   TYR A  35 
 PHE   0.008   0.001   PHE B 297 
 TRP   0.006   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4617)
  covalent geometry    : angle       0.57695 ( 6259)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.42461 (   10)
  hydrogen bonds       : bond        0.05249 (  188)
  hydrogen bonds       : angle       4.76060 (  528)
  link_BETA1-4         : bond        0.00386 (    3)
  link_BETA1-4         : angle       2.44329 (    9)
  link_NAG-ASN         : bond        0.00236 (    7)
  link_NAG-ASN         : angle       2.23971 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8815 (tpp) cc_final: 0.8538 (tpp)
REVERT: A  211 LYS cc_start: 0.7965 (tppp) cc_final: 0.7612 (ttpt)
  outliers start: 11
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0988
  time to fit residues: 7.4382
Evaluate side-chains
  55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  371 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0970
   chunk 38 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 108 HIS
A 149 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.098089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.083043 restraints weight = 11963.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.084963 restraints weight = 7589.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.086254 restraints weight = 5599.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.087152 restraints weight = 4556.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.087688 restraints weight = 3934.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4632  Z= 0.165
  Angle     :  0.631   5.914   6299  Z= 0.307
  Chirality :  0.044   0.183    729
  Planarity :  0.004   0.033    793
  Dihedral  :  6.554  57.474    805
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.27 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.36), residues: 543
  helix:  2.37 (0.46), residues: 128
  sheet: -0.23 (0.38), residues: 170
  loop : -1.13 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A  95 
 TRP   0.007   0.001   TRP B 269 
 HIS   0.010   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4617)
  covalent geometry    : angle       0.60628 ( 6259)
  SS BOND              : bond        0.00234 (    5)
  SS BOND              : angle       0.54299 (   10)
  hydrogen bonds       : bond        0.05924 (  188)
  hydrogen bonds       : angle       4.91300 (  528)
  link_BETA1-4         : bond        0.00246 (    3)
  link_BETA1-4         : angle       2.57246 (    9)
  link_NAG-ASN         : bond        0.00202 (    7)
  link_NAG-ASN         : angle       2.60296 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8858 (tpp) cc_final: 0.8558 (tpp)
REVERT: A  211 LYS cc_start: 0.8041 (tppp) cc_final: 0.7696 (ttpt)
  outliers start: 12
  outliers final: 7
  residues processed: 59
  average time/residue: 0.1122
  time to fit residues: 8.0901
Evaluate side-chains
  56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0060
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
A 149 ASN
B 193 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.099493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.084149 restraints weight = 12206.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.086116 restraints weight = 7759.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.087434 restraints weight = 5725.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.088329 restraints weight = 4659.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.088946 restraints weight = 4031.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4632  Z= 0.126
  Angle     :  0.600   5.692   6299  Z= 0.293
  Chirality :  0.043   0.155    729
  Planarity :  0.004   0.037    793
  Dihedral  :  6.182  56.535    805
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.26 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.36), residues: 543
  helix:  2.65 (0.46), residues: 128
  sheet: -0.21 (0.38), residues: 168
  loop : -1.02 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.009   0.001   TYR A  35 
 PHE   0.007   0.001   PHE B 297 
 TRP   0.004   0.001   TRP B 197 
 HIS   0.011   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4617)
  covalent geometry    : angle       0.57489 ( 6259)
  SS BOND              : bond        0.00162 (    5)
  SS BOND              : angle       0.73308 (   10)
  hydrogen bonds       : bond        0.05520 (  188)
  hydrogen bonds       : angle       4.70419 (  528)
  link_BETA1-4         : bond        0.00298 (    3)
  link_BETA1-4         : angle       2.50954 (    9)
  link_NAG-ASN         : bond        0.00222 (    7)
  link_NAG-ASN         : angle       2.52719 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8840 (tpp) cc_final: 0.8541 (tpp)
REVERT: A  211 LYS cc_start: 0.8030 (tppp) cc_final: 0.7702 (ttpt)
  outliers start: 15
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0892
  time to fit residues: 7.1013
Evaluate side-chains
  57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  193 ASN
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0570
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.083876 restraints weight = 12085.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.085848 restraints weight = 7681.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.087177 restraints weight = 5683.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.088060 restraints weight = 4620.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.088603 restraints weight = 4008.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4632  Z= 0.131
  Angle     :  0.605   5.488   6299  Z= 0.295
  Chirality :  0.043   0.159    729
  Planarity :  0.004   0.036    793
  Dihedral  :  6.050  56.135    805
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.07 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.37), residues: 543
  helix:  2.65 (0.46), residues: 128
  sheet: -0.20 (0.38), residues: 168
  loop : -1.01 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  54 
 TYR   0.008   0.001   TYR A  35 
 PHE   0.008   0.001   PHE B 292 
 TRP   0.006   0.001   TRP B 310 
 HIS   0.011   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4617)
  covalent geometry    : angle       0.58045 ( 6259)
  SS BOND              : bond        0.00166 (    5)
  SS BOND              : angle       0.67488 (   10)
  hydrogen bonds       : bond        0.05463 (  188)
  hydrogen bonds       : angle       4.70650 (  528)
  link_BETA1-4         : bond        0.00353 (    3)
  link_BETA1-4         : angle       2.53039 (    9)
  link_NAG-ASN         : bond        0.00199 (    7)
  link_NAG-ASN         : angle       2.53768 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.6153 (t)
REVERT: A  153 MET cc_start: 0.8846 (tpp) cc_final: 0.8540 (tpp)
REVERT: A  211 LYS cc_start: 0.8022 (tppp) cc_final: 0.7700 (ttpt)
  outliers start: 12
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0963
  time to fit residues: 7.1111
Evaluate side-chains
  57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0570
   chunk 26 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.099866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.084606 restraints weight = 12215.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.086606 restraints weight = 7711.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087971 restraints weight = 5672.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.088860 restraints weight = 4586.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.089461 restraints weight = 3965.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4632  Z= 0.121
  Angle     :  0.600   5.399   6299  Z= 0.295
  Chirality :  0.042   0.154    729
  Planarity :  0.004   0.039    793
  Dihedral  :  5.805  55.604    805
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.86 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.37), residues: 543
  helix:  2.75 (0.47), residues: 128
  sheet: -0.07 (0.39), residues: 165
  loop : -0.93 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  54 
 TYR   0.007   0.001   TYR A  35 
 PHE   0.008   0.001   PHE B 292 
 TRP   0.005   0.001   TRP B 310 
 HIS   0.012   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4617)
  covalent geometry    : angle       0.57592 ( 6259)
  SS BOND              : bond        0.00192 (    5)
  SS BOND              : angle       0.63810 (   10)
  hydrogen bonds       : bond        0.05169 (  188)
  hydrogen bonds       : angle       4.57611 (  528)
  link_BETA1-4         : bond        0.00356 (    3)
  link_BETA1-4         : angle       2.51391 (    9)
  link_NAG-ASN         : bond        0.00198 (    7)
  link_NAG-ASN         : angle       2.50454 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.6163 (t)
REVERT: A  153 MET cc_start: 0.8832 (tpp) cc_final: 0.8531 (tpp)
REVERT: A  211 LYS cc_start: 0.8013 (tppp) cc_final: 0.7677 (ttpt)
  outliers start: 11
  outliers final: 9
  residues processed: 56
  average time/residue: 0.0923
  time to fit residues: 6.4298
Evaluate side-chains
  56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0030
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5368

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.099883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.084689 restraints weight = 11946.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.086621 restraints weight = 7623.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.087936 restraints weight = 5660.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.088812 restraints weight = 4609.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.089359 restraints weight = 3994.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4632  Z= 0.122
  Angle     :  0.616   8.152   6299  Z= 0.300
  Chirality :  0.042   0.154    729
  Planarity :  0.004   0.038    793
  Dihedral  :  5.682  55.864    805
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 19.88 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.37), residues: 543
  helix:  2.72 (0.46), residues: 128
  sheet:  0.13 (0.40), residues: 159
  loop : -0.88 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  54 
 TYR   0.008   0.001   TYR B 186 
 PHE   0.009   0.001   PHE B 292 
 TRP   0.004   0.001   TRP B 197 
 HIS   0.013   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4617)
  covalent geometry    : angle       0.59318 ( 6259)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       0.58130 (   10)
  hydrogen bonds       : bond        0.05163 (  188)
  hydrogen bonds       : angle       4.55925 (  528)
  link_BETA1-4         : bond        0.00298 (    3)
  link_BETA1-4         : angle       2.51435 (    9)
  link_NAG-ASN         : bond        0.00187 (    7)
  link_NAG-ASN         : angle       2.48538 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6602 (OUTLIER) cc_final: 0.6192 (t)
REVERT: A  153 MET cc_start: 0.8830 (tpp) cc_final: 0.8529 (tpp)
REVERT: A  211 LYS cc_start: 0.7953 (tppp) cc_final: 0.7625 (ttpt)
  outliers start: 11
  outliers final: 8
  residues processed: 55
  average time/residue: 0.0892
  time to fit residues: 6.1967
Evaluate side-chains
  57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.0980
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0370
   chunk 14 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.100880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.085782 restraints weight = 11866.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.087752 restraints weight = 7506.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.089091 restraints weight = 5536.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.089999 restraints weight = 4488.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.090567 restraints weight = 3873.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4632  Z= 0.114
  Angle     :  0.605   7.528   6299  Z= 0.296
  Chirality :  0.042   0.148    729
  Planarity :  0.004   0.040    793
  Dihedral  :  5.473  55.452    805
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 19.68 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.37), residues: 543
  helix:  2.81 (0.46), residues: 129
  sheet:  0.18 (0.40), residues: 159
  loop : -0.81 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 176 
 TYR   0.007   0.001   TYR A  35 
 PHE   0.009   0.001   PHE B 292 
 TRP   0.005   0.001   TRP B 197 
 HIS   0.014   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4617)
  covalent geometry    : angle       0.58250 ( 6259)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       0.60678 (   10)
  hydrogen bonds       : bond        0.04805 (  188)
  hydrogen bonds       : angle       4.39733 (  528)
  link_BETA1-4         : bond        0.00409 (    3)
  link_BETA1-4         : angle       2.45911 (    9)
  link_NAG-ASN         : bond        0.00244 (    7)
  link_NAG-ASN         : angle       2.39415 (   21)

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

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

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1086 Ramachandran restraints generated.
    543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.6195 (t)
REVERT: A  153 MET cc_start: 0.8811 (tpp) cc_final: 0.8530 (tpp)
REVERT: A  211 LYS cc_start: 0.7900 (tppp) cc_final: 0.7583 (ttpt)
REVERT: C  379 TYR cc_start: 0.8066 (p90) cc_final: 0.7746 (p90)
  outliers start: 11
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0802
  time to fit residues: 6.1163
Evaluate side-chains
  58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  209 PHE
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  172 CYS
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  318 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0000
   chunk 4 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0010
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
** C 338 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 = 0.3721 r_free = 0.3721 target = 0.100684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.085390 restraints weight = 12113.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087323 restraints weight = 7665.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.088709 restraints weight = 5709.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.089641 restraints weight = 4625.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.090290 restraints weight = 3988.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4632  Z= 0.116
  Angle     :  0.612   8.412   6299  Z= 0.297
  Chirality :  0.042   0.157    729
  Planarity :  0.004   0.038    793
  Dihedral  :  5.376  55.663    805
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.86 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.37), residues: 543
  helix:  2.83 (0.45), residues: 129
  sheet:  0.14 (0.40), residues: 164
  loop : -0.66 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  75 
 TYR   0.007   0.001   TYR B 186 
 PHE   0.007   0.001   PHE B 297 
 TRP   0.007   0.001   TRP B 197 
 HIS   0.008   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4617)
  covalent geometry    : angle       0.59106 ( 6259)
  SS BOND              : bond        0.00213 (    5)
  SS BOND              : angle       0.55899 (   10)
  hydrogen bonds       : bond        0.04855 (  188)
  hydrogen bonds       : angle       4.40381 (  528)
  link_BETA1-4         : bond        0.00386 (    3)
  link_BETA1-4         : angle       2.45064 (    9)
  link_NAG-ASN         : bond        0.00240 (    7)
  link_NAG-ASN         : angle       2.36904 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1123.01 seconds
wall clock time: 20 minutes 5.35 seconds (1205.35 seconds total)