Starting phenix.real_space_refine
on Sat May 10 01:38:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v2a_42903/05_2025/8v2a_42903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v2a_42903/05_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_42903/05_2025/8v2a_42903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v2a_42903/05_2025/8v2a_42903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v2a_42903/05_2025/8v2a_42903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v2a_42903/05_2025/8v2a_42903.cif"
  }
  resolution = 3.59
  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=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.94, per 1000 atoms: 0.87
  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: 1.21
  Conformation dependent library (CDL) restraints added in 537.3 milliseconds
  

  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: 0.56
  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: 1.18

  Time building geometry restraints manager: 1.41 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:             3.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.620
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.650
-------------------------------------------------------------------------------
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 (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: -1.69 (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
 TRP   0.014   0.001   TRP A 212 
 HIS   0.002   0.000   HIS A 199 
 PHE   0.005   0.001   PHE C 408 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.001   0.000   ARG B 262 

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

*********************** 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  : 0.495 
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: 0.2384
  time to fit residues: 24.4358
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  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0770
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0980
   chunk 49 optimal weight:   30.0000
   overall best weight:    0.9942

-------------------------------------------------------------------------------
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 = 0.3851 r_free = 0.3851 target = 0.104913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.089467 restraints weight = 11873.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.091556 restraints weight = 7494.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.092973 restraints weight = 5559.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4632  Z= 0.163
  Angle     :  0.643   6.404   6299  Z= 0.320
  Chirality :  0.045   0.188    729
  Planarity :  0.004   0.038    793
  Dihedral  : 13.352  78.416    805
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.98 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.35), residues: 543
  helix:  1.86 (0.47), residues: 127
  sheet: -0.77 (0.37), residues: 161
  loop : -1.61 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 212 
 HIS   0.009   0.001   HIS A 108 
 PHE   0.008   0.001   PHE C 316 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.005   0.000   ARG C 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       1.92363 (   21)
  link_BETA1-4         : bond        0.00283 (    3)
  link_BETA1-4         : angle       2.34753 (    9)
  hydrogen bonds       : bond        0.05846 (  188)
  hydrogen bonds       : angle       5.48382 (  528)
  SS BOND              : bond        0.00191 (    5)
  SS BOND              : angle       0.47571 (   10)
  covalent geometry    : bond        0.00368 ( 4617)
  covalent geometry    : angle       0.62911 ( 6259)

*********************** 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
  68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.6977 (tptm) cc_final: 0.6723 (tptm)
REVERT: A  153 MET cc_start: 0.8782 (tpp) cc_final: 0.8507 (tpp)
REVERT: A  211 LYS cc_start: 0.7961 (tppp) cc_final: 0.7652 (ttpt)
REVERT: C  320 ASP cc_start: 0.7856 (m-30) cc_final: 0.7650 (m-30)
  outliers start: 11
  outliers final: 6
  residues processed: 63
  average time/residue: 0.1843
  time to fit residues: 14.5674
Evaluate side-chains
  55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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 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 53 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0050
   chunk 17 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0570
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5312

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C 313 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.105417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.090217 restraints weight = 11911.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.092317 restraints weight = 7436.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.093771 restraints weight = 5470.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2024

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= 0.128
  Angle     :  0.618   7.524   6299  Z= 0.300
  Chirality :  0.044   0.183    729
  Planarity :  0.004   0.031    793
  Dihedral  : 10.295  58.508    805
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.01 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.36), residues: 543
  helix:  2.38 (0.46), residues: 126
  sheet: -0.36 (0.38), residues: 162
  loop : -1.34 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 212 
 HIS   0.009   0.001   HIS A 108 
 PHE   0.007   0.001   PHE B 297 
 TYR   0.009   0.001   TYR B 186 
 ARG   0.002   0.000   ARG C 381 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    7)
  link_NAG-ASN         : angle       2.01983 (   21)
  link_BETA1-4         : bond        0.00408 (    3)
  link_BETA1-4         : angle       2.41022 (    9)
  hydrogen bonds       : bond        0.05337 (  188)
  hydrogen bonds       : angle       5.02938 (  528)
  SS BOND              : bond        0.00146 (    5)
  SS BOND              : angle       0.42716 (   10)
  covalent geometry    : bond        0.00274 ( 4617)
  covalent geometry    : angle       0.60186 ( 6259)

*********************** 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
  65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8774 (tpp) cc_final: 0.8505 (tpp)
REVERT: A  211 LYS cc_start: 0.7953 (tppp) cc_final: 0.7627 (ttpt)
REVERT: C  320 ASP cc_start: 0.7927 (m-30) cc_final: 0.7654 (m-30)
REVERT: C  349 ILE cc_start: 0.7738 (mt) cc_final: 0.7463 (tt)
  outliers start: 12
  outliers final: 6
  residues processed: 60
  average time/residue: 0.1906
  time to fit residues: 14.4423
Evaluate side-chains
  53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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  236 LEU
Chi-restraints excluded: chain B residue  299 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.0030
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.104349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.089116 restraints weight = 12178.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.091226 restraints weight = 7530.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.092610 restraints weight = 5527.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2417

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     :  0.615   6.977   6299  Z= 0.297
  Chirality :  0.043   0.143    729
  Planarity :  0.004   0.033    793
  Dihedral  :  7.404  56.443    805
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.84 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.36), residues: 543
  helix:  2.37 (0.46), residues: 128
  sheet: -0.18 (0.39), residues: 163
  loop : -1.17 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 212 
 HIS   0.010   0.001   HIS A 108 
 PHE   0.009   0.001   PHE C 408 
 TYR   0.008   0.001   TYR A  35 
 ARG   0.002   0.000   ARG A  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    7)
  link_NAG-ASN         : angle       2.31429 (   21)
  link_BETA1-4         : bond        0.00320 (    3)
  link_BETA1-4         : angle       2.37869 (    9)
  hydrogen bonds       : bond        0.05341 (  188)
  hydrogen bonds       : angle       4.82663 (  528)
  SS BOND              : bond        0.00184 (    5)
  SS BOND              : angle       0.41620 (   10)
  covalent geometry    : bond        0.00293 ( 4617)
  covalent geometry    : angle       0.59571 ( 6259)

*********************** 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
  65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8791 (tpp) cc_final: 0.8506 (tpp)
REVERT: A  211 LYS cc_start: 0.7990 (tppp) cc_final: 0.7635 (ttpt)
REVERT: C  320 ASP cc_start: 0.7960 (m-30) cc_final: 0.7638 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 62
  average time/residue: 0.1878
  time to fit residues: 14.6704
Evaluate side-chains
  54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
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 30 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0970
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.098960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.083629 restraints weight = 12234.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.085600 restraints weight = 7790.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.086968 restraints weight = 5751.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2599

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= 0.150
  Angle     :  0.643   8.764   6299  Z= 0.309
  Chirality :  0.043   0.153    729
  Planarity :  0.004   0.034    793
  Dihedral  :  6.580  57.430    805
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.02
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.36), residues: 543
  helix:  2.39 (0.46), residues: 128
  sheet: -0.09 (0.39), residues: 163
  loop : -1.14 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 212 
 HIS   0.011   0.001   HIS A 108 
 PHE   0.008   0.001   PHE B 297 
 TYR   0.009   0.001   TYR A 198 
 ARG   0.003   0.000   ARG A  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    7)
  link_NAG-ASN         : angle       2.59226 (   21)
  link_BETA1-4         : bond        0.00272 (    3)
  link_BETA1-4         : angle       2.47046 (    9)
  hydrogen bonds       : bond        0.05623 (  188)
  hydrogen bonds       : angle       4.83000 (  528)
  SS BOND              : bond        0.00473 (    5)
  SS BOND              : angle       0.47508 (   10)
  covalent geometry    : bond        0.00346 ( 4617)
  covalent geometry    : angle       0.61999 ( 6259)

*********************** 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
  69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6859 (tptm)
REVERT: A  153 MET cc_start: 0.8804 (tpp) cc_final: 0.8500 (tpp)
REVERT: A  211 LYS cc_start: 0.8055 (tppp) cc_final: 0.7675 (ttpt)
REVERT: C  320 ASP cc_start: 0.7882 (m-30) cc_final: 0.7503 (m-30)
REVERT: C  347 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6925 (mmtt)
  outliers start: 15
  outliers final: 8
  residues processed: 64
  average time/residue: 0.2107
  time to fit residues: 16.6899
Evaluate side-chains
  57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0170
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:   40.0000
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7222

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.099171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.083960 restraints weight = 12161.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.085922 restraints weight = 7741.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087246 restraints weight = 5715.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4632  Z= 0.138
  Angle     :  0.629   6.964   6299  Z= 0.307
  Chirality :  0.043   0.154    729
  Planarity :  0.004   0.037    793
  Dihedral  :  6.327  57.099    805
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 18.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.36), residues: 543
  helix:  2.54 (0.46), residues: 128
  sheet: -0.20 (0.39), residues: 166
  loop : -1.03 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 212 
 HIS   0.010   0.001   HIS A 108 
 PHE   0.009   0.001   PHE C 397 
 TYR   0.008   0.001   TYR A  35 
 ARG   0.003   0.000   ARG B 143 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    7)
  link_NAG-ASN         : angle       2.57167 (   21)
  link_BETA1-4         : bond        0.00325 (    3)
  link_BETA1-4         : angle       2.48750 (    9)
  hydrogen bonds       : bond        0.05558 (  188)
  hydrogen bonds       : angle       4.76369 (  528)
  SS BOND              : bond        0.00359 (    5)
  SS BOND              : angle       1.09924 (   10)
  covalent geometry    : bond        0.00318 ( 4617)
  covalent geometry    : angle       0.60382 ( 6259)

*********************** 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
  66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6166 (t)
REVERT: A  153 MET cc_start: 0.8800 (tpp) cc_final: 0.8491 (tpp)
REVERT: A  211 LYS cc_start: 0.8036 (tppp) cc_final: 0.7669 (ttpt)
REVERT: B  293 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7036 (p)
REVERT: C  320 ASP cc_start: 0.7879 (m-30) cc_final: 0.7463 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1904
  time to fit residues: 14.7279
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  : 0.541 
-------------------------------------------------------------------------------
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  293 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.098592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.083510 restraints weight = 12038.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.085435 restraints weight = 7712.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.086726 restraints weight = 5727.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2857

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= 0.146
  Angle     :  0.631   5.831   6299  Z= 0.309
  Chirality :  0.043   0.161    729
  Planarity :  0.004   0.035    793
  Dihedral  :  6.131  57.036    805
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.37), residues: 543
  helix:  2.52 (0.46), residues: 128
  sheet: -0.14 (0.39), residues: 166
  loop : -0.98 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 212 
 HIS   0.012   0.001   HIS A 108 
 PHE   0.007   0.001   PHE B 297 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.002   0.000   ARG A  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00202 (    7)
  link_NAG-ASN         : angle       2.61076 (   21)
  link_BETA1-4         : bond        0.00309 (    3)
  link_BETA1-4         : angle       2.54945 (    9)
  hydrogen bonds       : bond        0.05696 (  188)
  hydrogen bonds       : angle       4.81643 (  528)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       0.69875 (   10)
  covalent geometry    : bond        0.00333 ( 4617)
  covalent geometry    : angle       0.60668 ( 6259)

*********************** 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: 15
    poor density    : 49
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6620 (OUTLIER) cc_final: 0.6165 (t)
REVERT: A  153 MET cc_start: 0.8793 (tpp) cc_final: 0.8502 (tpp)
REVERT: A  211 LYS cc_start: 0.8033 (tppp) cc_final: 0.7706 (ttpt)
REVERT: B  293 THR cc_start: 0.7357 (OUTLIER) cc_final: 0.7106 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 60
  average time/residue: 0.1855
  time to fit residues: 14.2233
Evaluate side-chains
  58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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  293 THR
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  420 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3694 r_free = 0.3694 target = 0.098946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.083779 restraints weight = 12089.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.085712 restraints weight = 7741.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.087030 restraints weight = 5726.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2976

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= 0.133
  Angle     :  0.633   6.119   6299  Z= 0.308
  Chirality :  0.043   0.160    729
  Planarity :  0.004   0.037    793
  Dihedral  :  5.978  56.959    805
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 18.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.37), residues: 543
  helix:  2.62 (0.46), residues: 128
  sheet: -0.11 (0.40), residues: 166
  loop : -0.93 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 212 
 HIS   0.013   0.001   HIS A 108 
 PHE   0.007   0.001   PHE B 297 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    7)
  link_NAG-ASN         : angle       2.56965 (   21)
  link_BETA1-4         : bond        0.00315 (    3)
  link_BETA1-4         : angle       2.53392 (    9)
  hydrogen bonds       : bond        0.05485 (  188)
  hydrogen bonds       : angle       4.72709 (  528)
  SS BOND              : bond        0.00229 (    5)
  SS BOND              : angle       0.62408 (   10)
  covalent geometry    : bond        0.00298 ( 4617)
  covalent geometry    : angle       0.60944 ( 6259)

*********************** 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
  66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6591 (OUTLIER) cc_final: 0.6164 (t)
REVERT: A  153 MET cc_start: 0.8804 (tpp) cc_final: 0.8495 (tpp)
REVERT: A  211 LYS cc_start: 0.8021 (tppp) cc_final: 0.7703 (ttpt)
REVERT: B  293 THR cc_start: 0.7302 (OUTLIER) cc_final: 0.7005 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 62
  average time/residue: 0.2060
  time to fit residues: 15.9427
Evaluate side-chains
  59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
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  293 THR
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  420 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0570
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.100145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.085076 restraints weight = 12082.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.087032 restraints weight = 7686.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.088324 restraints weight = 5677.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3014

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= 0.126
  Angle     :  0.649   9.741   6299  Z= 0.317
  Chirality :  0.042   0.152    729
  Planarity :  0.004   0.038    793
  Dihedral  :  5.736  56.187    805
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.88 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.37), residues: 543
  helix:  2.75 (0.46), residues: 128
  sheet: -0.02 (0.40), residues: 165
  loop : -0.87 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 212 
 HIS   0.013   0.001   HIS A 108 
 PHE   0.007   0.001   PHE B 297 
 TYR   0.008   0.001   TYR C 379 
 ARG   0.001   0.000   ARG A 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    7)
  link_NAG-ASN         : angle       2.52824 (   21)
  link_BETA1-4         : bond        0.00370 (    3)
  link_BETA1-4         : angle       2.48133 (    9)
  hydrogen bonds       : bond        0.05091 (  188)
  hydrogen bonds       : angle       4.54912 (  528)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.62385 (   10)
  covalent geometry    : bond        0.00284 ( 4617)
  covalent geometry    : angle       0.62733 ( 6259)

*********************** 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
  61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.6169 (t)
REVERT: A  153 MET cc_start: 0.8785 (tpp) cc_final: 0.8488 (tpp)
REVERT: A  211 LYS cc_start: 0.7981 (tppp) cc_final: 0.7660 (ttpt)
REVERT: B  293 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6913 (p)
  outliers start: 12
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1891
  time to fit residues: 13.9019
Evaluate side-chains
  56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
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  293 THR
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  348 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.099175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.084077 restraints weight = 12014.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.086007 restraints weight = 7679.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087305 restraints weight = 5701.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.3098

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= 0.136
  Angle     :  0.656   9.131   6299  Z= 0.323
  Chirality :  0.043   0.184    729
  Planarity :  0.004   0.038    793
  Dihedral  :  5.677  56.771    805
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.69 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.37), residues: 543
  helix:  2.66 (0.46), residues: 128
  sheet:  0.18 (0.41), residues: 159
  loop : -0.85 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 212 
 HIS   0.008   0.001   HIS A 108 
 PHE   0.008   0.001   PHE B 297 
 TYR   0.008   0.001   TYR A  35 
 ARG   0.001   0.000   ARG A  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00206 (    7)
  link_NAG-ASN         : angle       2.52600 (   21)
  link_BETA1-4         : bond        0.00330 (    3)
  link_BETA1-4         : angle       2.50750 (    9)
  hydrogen bonds       : bond        0.05313 (  188)
  hydrogen bonds       : angle       4.60927 (  528)
  SS BOND              : bond        0.00207 (    5)
  SS BOND              : angle       0.57909 (   10)
  covalent geometry    : bond        0.00308 ( 4617)
  covalent geometry    : angle       0.63441 ( 6259)

********************** 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
  56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6205 (t)
REVERT: A  153 MET cc_start: 0.8810 (tpp) cc_final: 0.8499 (tpp)
REVERT: A  211 LYS cc_start: 0.8014 (tppp) cc_final: 0.7703 (ttpt)
REVERT: B  293 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.6972 (p)
REVERT: C  379 TYR cc_start: 0.8130 (p90) cc_final: 0.7819 (p90)
  outliers start: 10
  outliers final: 7
  residues processed: 53
  average time/residue: 0.1871
  time to fit residues: 12.5709
Evaluate side-chains
  52 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
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  293 THR
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 11 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0020
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4588

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.100141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.084974 restraints weight = 12029.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.086894 restraints weight = 7669.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.088246 restraints weight = 5698.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3168

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= 0.124
  Angle     :  0.658   8.817   6299  Z= 0.318
  Chirality :  0.042   0.153    729
  Planarity :  0.004   0.038    793
  Dihedral  :  5.485  56.219    805
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.49 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.37), residues: 543
  helix:  2.78 (0.46), residues: 128
  sheet:  0.28 (0.41), residues: 158
  loop : -0.82 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 212 
 HIS   0.008   0.001   HIS A 108 
 PHE   0.007   0.001   PHE B 297 
 TYR   0.009   0.001   TYR C 331 
 ARG   0.001   0.000   ARG C 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00224 (    7)
  link_NAG-ASN         : angle       2.46616 (   21)
  link_BETA1-4         : bond        0.00373 (    3)
  link_BETA1-4         : angle       2.46947 (    9)
  hydrogen bonds       : bond        0.05014 (  188)
  hydrogen bonds       : angle       4.46769 (  528)
  SS BOND              : bond        0.00204 (    5)
  SS BOND              : angle       0.59034 (   10)
  covalent geometry    : bond        0.00275 ( 4617)
  covalent geometry    : angle       0.63767 ( 6259)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.90 seconds
wall clock time: 33 minutes 38.40 seconds (2018.40 seconds total)