Starting phenix.real_space_refine
on Tue Jan 14 11:23:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.cif"
  }
  resolution = 2.9
  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=   0.004 sd=   0.254
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: 5
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     Cl      2      4.86       5
     C    4310      2.51       5
     N    1145      2.21       5
     O    1236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6719
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3254
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3254
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 61
    Chain: "B"
      Number of atoms: 3257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3257
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 56
    Chain: "C"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          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: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          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: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' CL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' CL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 4.63, per 1000 atoms: 0.69
  Number of scatterers: 6719
  At special positions: 0
  Unit cell: (106.095, 77.9472, 84.4428, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      26     16.00
     O    1236      8.00
     N    1145      7.00
     C    4310      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  86 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 213 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " NAG C   2 " - " MAN C   3 "
      " NAG D   2 " - " MAN D   3 "
      " NAG E   2 " - " MAN E   3 "
      " NAG F   2 " - " MAN F   3 "
    ALPHA1-6
      " MAN C   3 " - " MAN C   4 "
      " MAN E   3 " - " MAN E   4 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1102 " - " ASN A 354 "
      " NAG B1102 " - " ASN B 354 "
      " NAG C   1 " - " ASN A  13 "
      " NAG D   1 " - " ASN A 395 "
      " NAG E   1 " - " ASN B  13 "
      " NAG F   1 " - " ASN B 395 "
  Time building additional restraints: 2.24
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      42.8% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 36
      Proline residue:  A  25  - end of helix
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 86 through 101
      removed outlier: 3.889A  pdb=" N   ALA A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 112 through 116
      removed outlier: 3.623A  pdb=" N   VAL A 116 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 145
      removed outlier: 4.040A  pdb=" N   GLY A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASP A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 136 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 179
    Processing helix  chain 'A' and resid 192 through 207
      removed outlier: 3.693A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 215 through 230
      removed outlier: 3.565A  pdb=" N   LEU A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 249
      removed outlier: 3.912A  pdb=" N   GLN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 274
      removed outlier: 3.793A  pdb=" N   GLN A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 306
      removed outlier: 3.564A  pdb=" N   LEU A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   HIS A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   LEU A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 338
    Processing helix  chain 'A' and resid 344 through 350
    Processing helix  chain 'B' and resid 19 through 35
      Proline residue:  B  25  - end of helix
    Processing helix  chain 'B' and resid 64 through 77
    Processing helix  chain 'B' and resid 86 through 101
      removed outlier: 3.868A  pdb=" N   ALA B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
    Processing helix  chain 'B' and resid 112 through 116
      removed outlier: 3.647A  pdb=" N   VAL B 116 " --> pdb=" O   GLY B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 145
      removed outlier: 3.765A  pdb=" N   ASP B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE B 136 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL B 137 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 179
      removed outlier: 3.532A  pdb=" N   ASP B 177 " --> pdb=" O   MET B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 215 through 230
    Processing helix  chain 'B' and resid 245 through 249
      removed outlier: 3.814A  pdb=" N   GLN B 249 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 274
      removed outlier: 4.086A  pdb=" N   GLN B 272 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA B 273 " --> pdb=" O   SER B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 304
      removed outlier: 3.671A  pdb=" N   LEU B 291 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   HIS B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU B 300 " --> pdb=" O   GLN B 296 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR B 302 " --> pdb=" O   LYS B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 338
      removed outlier: 3.542A  pdb=" N   HIS B 322 " --> pdb=" O   PRO B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 351
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51
      removed outlier: 9.101A  pdb=" N   VAL A  80 " --> pdb=" O   ASN A   2 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   THR A   4 " --> pdb=" O   VAL A  80 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   LEU A  82 " --> pdb=" O   THR A   4 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA A   6 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   PHE A  81 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU A 104 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189
      removed outlier: 5.240A  pdb=" N   VAL A 209 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ILE A 210 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   LEU A 241 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   PHE A 238 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   ILE A 280 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   HIS A 240 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 8.352A  pdb=" N   TYR A 282 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ALA A 277 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   MET A 381 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ASP A 380 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLU A 400 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 359
      removed outlier: 3.726A  pdb=" N   GLY A 362 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.273A  pdb=" N   LEU B   3 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   VAL B  49 " --> pdb=" O   LEU B   3 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B   5 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   GLY B  51 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   VAL B   7 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   LEU B  82 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ALA B   6 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   PHE B  81 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   LEU B 104 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 189
      removed outlier: 6.933A  pdb=" N   ALA B 150 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 150 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   MET B 152 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   PHE B 188 " --> pdb=" O   MET B 152 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR B 154 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   VAL B 209 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   PHE B 238 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   ILE B 280 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   HIS B 240 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
      removed outlier: 8.341A  pdb=" N   TYR B 282 " --> pdb=" O   HIS B 240 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ALA B 277 " --> pdb=" O   MET B 381 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   MET B 381 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   PHE B 376 " --> pdb=" O   ASN B 393 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ASN B 393 " --> pdb=" O   PHE B 376 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 378 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 355 through 359
      removed outlier: 3.663A  pdb=" N   GLY B 362 " --> pdb=" O   GLY B 359 " (cutoff:3.500A)

    277 hydrogen bonds defined for protein.
    807 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: 1.84

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1054
        1.29 -     1.42: 1897
        1.42 -     1.56: 3909
        1.56 -     1.69: 3
        1.69 -     1.83: 40
  Bond restraints: 6903
  Sorted by residual:
  bond pdb=" C   ASP B 375 "
       pdb=" O   ASP B 375 "
    ideal  model  delta    sigma   weight residual
    1.235  1.155  0.080 1.18e-02 7.18e+03 4.56e+01
  bond pdb=" C   HIS A 185 "
       pdb=" O   HIS A 185 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.055 1.14e-02 7.69e+03 2.32e+01
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.481 -0.075 2.00e-02 2.50e+03 1.40e+01
  bond pdb=" C   GLU B 373 "
       pdb=" O   GLU B 373 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.17e-02 7.31e+03 1.10e+01
  bond pdb=" C   GLU A 373 "
       pdb=" O   GLU A 373 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.037 1.21e-02 6.83e+03 9.20e+00
  ... (remaining 6898 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9208
        2.19 -     4.38: 174
        4.38 -     6.57: 34
        6.57 -     8.76: 2
        8.76 -    10.94: 3
  Bond angle restraints: 9421
  Sorted by residual:
  angle pdb=" CA  HIS A 185 "
        pdb=" CB  HIS A 185 "
        pdb=" CG  HIS A 185 "
      ideal   model   delta    sigma   weight residual
     113.80  120.56   -6.76 1.00e+00 1.00e+00 4.58e+01
  angle pdb=" CA  THR A  14 "
        pdb=" CB  THR A  14 "
        pdb=" CG2 THR A  14 "
      ideal   model   delta    sigma   weight residual
     110.50  119.84   -9.34 1.70e+00 3.46e-01 3.02e+01
  angle pdb=" OG1 THR A  14 "
        pdb=" CB  THR A  14 "
        pdb=" CG2 THR A  14 "
      ideal   model   delta    sigma   weight residual
     109.30  120.24  -10.94 2.00e+00 2.50e-01 2.99e+01
  angle pdb=" CA  HIS A 185 "
        pdb=" C   HIS A 185 "
        pdb=" O   HIS A 185 "
      ideal   model   delta    sigma   weight residual
     120.40  115.38    5.02 1.05e+00 9.07e-01 2.29e+01
  angle pdb=" CA  GLN B 252 "
        pdb=" CB  GLN B 252 "
        pdb=" CG  GLN B 252 "
      ideal   model   delta    sigma   weight residual
     114.10  123.42   -9.32 2.00e+00 2.50e-01 2.17e+01
  ... (remaining 9416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.51: 4004
       23.51 -    47.02: 181
       47.02 -    70.52: 25
       70.52 -    94.03: 18
       94.03 -   117.54: 3
  Dihedral angle restraints: 4231
    sinusoidal: 1803
      harmonic: 2428
  Sorted by residual:
  dihedral pdb=" CA  LEU A  82 "
           pdb=" C   LEU A  82 "
           pdb=" N   GLY A  83 "
           pdb=" CA  GLY A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.87  -25.13     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" N   GLU B 373 "
           pdb=" C   GLU B 373 "
           pdb=" CA  GLU B 373 "
           pdb=" CB  GLU B 373 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.15   11.65     0      2.50e+00 1.60e-01 2.17e+01
  dihedral pdb=" CB  CYS B  60 "
           pdb=" SG  CYS B  60 "
           pdb=" SG  CYS B  86 "
           pdb=" CB  CYS B  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.58  -36.58     1      1.00e+01 1.00e-02 1.89e+01
  ... (remaining 4228 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.300: 1074
       0.300 -    0.599: 2
       0.599 -    0.899: 0
       0.899 -    1.198: 0
       1.198 -    1.498: 1
  Chirality restraints: 1077
  Sorted by residual:
  chirality pdb=" CB  THR A  14 "
            pdb=" CA  THR A  14 "
            pdb=" OG1 THR A  14 "
            pdb=" CG2 THR A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.05    1.50 2.00e-01 2.50e+01 5.61e+01
  chirality pdb=" CA  GLU B 373 "
            pdb=" N   GLU B 373 "
            pdb=" C   GLU B 373 "
            pdb=" CB  GLU B 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.35e+00
  chirality pdb=" C4  NAG F   1 "
            pdb=" C3  NAG F   1 "
            pdb=" C5  NAG F   1 "
            pdb=" O4  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.17   -0.36 2.00e-01 2.50e+01 3.20e+00
  ... (remaining 1074 not shown)

  Planarity restraints: 1205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 420 "    0.047 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO A 421 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 421 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 421 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 372 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   ARG B 372 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ARG B 372 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU B 373 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 317 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO B 318 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 318 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 318 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1202 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 143
        2.70 -     3.25: 6459
        3.25 -     3.80: 10202
        3.80 -     4.35: 14131
        4.35 -     4.90: 23658
  Nonbonded interactions: 54593
  Sorted by model distance:
  nonbonded pdb=" O3  NAG E   2 "
            pdb=" O7  NAG E   2 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   ARG B 257 "
            pdb=" N   PHE B 388 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O4  NAG C   1 "
            pdb=" O7  NAG C   2 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" O   ARG B 176 "
            pdb=" O   LEU B 179 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   ASN A  13 "
            pdb=" OG  SER A  19 "
     model   vdw
     2.409 3.040
  ... (remaining 54588 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 419 or (resid 420 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 421 through 425 or resid 1101 through 1102)) \ 

  selection = (chain 'B' and (resid 1 through 204 or (resid 205 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 206 through 425 or resid 1101 through 1102)) \ 

}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     19.540
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
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      :  0.005   0.080   6903  Z= 0.346
  Angle     :  0.756  10.945   9421  Z= 0.405
  Chirality :  0.067   1.498   1077
  Planarity :  0.005   0.072   1199
  Dihedral  : 14.783 117.541   2671
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.15 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.28), residues: 846
  helix:  0.12 (0.30), residues: 310
  sheet: -1.49 (0.36), residues: 190
  loop : -1.47 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 379 
 HIS   0.017   0.002   HIS A 185 
 PHE   0.021   0.001   PHE B 172 
 TYR   0.026   0.001   TYR B 236 
 ARG   0.005   0.000   ARG B 208 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.611 
Fit side-chains
REVERT: A    2 ASN cc_start: 0.8268 (m-40) cc_final: 0.8010 (m-40)
REVERT: A  161 GLU cc_start: 0.7636 (mp0) cc_final: 0.7367 (mp0)
REVERT: A  182 THR cc_start: 0.8198 (m) cc_final: 0.7941 (p)
REVERT: A  185 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7553 (p90)
REVERT: A  192 ASP cc_start: 0.7377 (t70) cc_final: 0.7125 (OUTLIER)
REVERT: B  298 LYS cc_start: 0.8122 (mttm) cc_final: 0.7897 (mptm)
  outliers start: 2
  outliers final: 1
  residues processed: 109
  average time/residue: 1.1621
  time to fit residues: 133.6629
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    0.3980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 163 HIS
A 185 HIS
B 163 HIS
B 322 HIS
B 338 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.145392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.114251 restraints weight = 7441.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.18
r_work: 0.3158 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6903  Z= 0.213
  Angle     :  0.670   9.828   9421  Z= 0.316
  Chirality :  0.044   0.322   1077
  Planarity :  0.005   0.046   1199
  Dihedral  : 10.915 110.086   1257
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  7.28 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 846
  helix:  1.10 (0.30), residues: 314
  sheet: -1.27 (0.35), residues: 190
  loop : -1.30 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 379 
 HIS   0.008   0.001   HIS A 322 
 PHE   0.019   0.001   PHE B 172 
 TYR   0.013   0.001   TYR B 154 
 ARG   0.006   0.000   ARG A 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A    2 ASN cc_start: 0.8366 (m-40) cc_final: 0.8127 (m-40)
REVERT: A  161 GLU cc_start: 0.8056 (mp0) cc_final: 0.7812 (mp0)
REVERT: A  182 THR cc_start: 0.8020 (m) cc_final: 0.7723 (p)
REVERT: A  232 CYS cc_start: 0.8354 (p) cc_final: 0.7958 (p)
REVERT: A  234 GLU cc_start: 0.8314 (mp0) cc_final: 0.7820 (mp0)
REVERT: A  419 ASP cc_start: 0.8038 (p0) cc_final: 0.7397 (t0)
REVERT: B  179 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7815 (mt)
  outliers start: 10
  outliers final: 1
  residues processed: 84
  average time/residue: 1.1068
  time to fit residues: 98.9307
Evaluate side-chains
  70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain B residue  179 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  33 GLN
A 195 HIS
B 338 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.108701 restraints weight = 7667.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.21
r_work: 0.3078 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   6903  Z= 0.467
  Angle     :  0.760  10.054   9421  Z= 0.356
  Chirality :  0.050   0.354   1077
  Planarity :  0.005   0.041   1199
  Dihedral  : 10.185 101.113   1255
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.44 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.29), residues: 846
  helix:  1.12 (0.30), residues: 314
  sheet: -1.06 (0.36), residues: 190
  loop : -1.32 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 379 
 HIS   0.008   0.002   HIS B 322 
 PHE   0.021   0.002   PHE B 172 
 TYR   0.017   0.002   TYR B 154 
 ARG   0.005   0.001   ARG A 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.8385 (m-40) cc_final: 0.8153 (m-40)
REVERT: A  161 GLU cc_start: 0.8128 (mp0) cc_final: 0.7822 (mp0)
REVERT: A  192 ASP cc_start: 0.7254 (t70) cc_final: 0.6809 (t0)
REVERT: A  232 CYS cc_start: 0.8503 (p) cc_final: 0.8287 (p)
REVERT: B  232 CYS cc_start: 0.8472 (p) cc_final: 0.8212 (p)
  outliers start: 13
  outliers final: 6
  residues processed: 84
  average time/residue: 0.9942
  time to fit residues: 89.4188
Evaluate side-chains
  78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
A 322 HIS
B 338 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.112425 restraints weight = 7536.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.23
r_work: 0.3154 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6903  Z= 0.198
  Angle     :  0.637   8.459   9421  Z= 0.294
  Chirality :  0.043   0.299   1077
  Planarity :  0.004   0.040   1199
  Dihedral  :  9.304 101.152   1255
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.00 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.29), residues: 846
  helix:  1.55 (0.30), residues: 314
  sheet: -0.74 (0.37), residues: 178
  loop : -1.26 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 379 
 HIS   0.013   0.001   HIS A 185 
 PHE   0.014   0.001   PHE B 172 
 TYR   0.012   0.001   TYR A 154 
 ARG   0.007   0.000   ARG A 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.8374 (m-40) cc_final: 0.8147 (m-40)
REVERT: A   75 GLU cc_start: 0.8253 (tt0) cc_final: 0.7676 (tp30)
REVERT: A  161 GLU cc_start: 0.7930 (mp0) cc_final: 0.7726 (mp0)
REVERT: A  232 CYS cc_start: 0.8356 (p) cc_final: 0.8143 (p)
REVERT: A  419 ASP cc_start: 0.7991 (p0) cc_final: 0.7358 (t0)
REVERT: B   75 GLU cc_start: 0.8362 (tt0) cc_final: 0.7825 (tp30)
REVERT: B  152 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8444 (mtt)
REVERT: B  232 CYS cc_start: 0.8429 (p) cc_final: 0.8137 (p)
  outliers start: 6
  outliers final: 3
  residues processed: 84
  average time/residue: 0.9440
  time to fit residues: 84.9391
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain B residue  152 MET
Chi-restraints excluded: chain B residue  311 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
A 299 HIS
B 338 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.110292 restraints weight = 7553.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.21
r_work: 0.3120 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6903  Z= 0.288
  Angle     :  0.659   9.520   9421  Z= 0.306
  Chirality :  0.045   0.313   1077
  Planarity :  0.005   0.037   1199
  Dihedral  :  9.022  97.843   1255
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.38 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.29), residues: 846
  helix:  1.60 (0.30), residues: 314
  sheet: -0.72 (0.36), residues: 178
  loop : -1.26 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 379 
 HIS   0.007   0.002   HIS A 185 
 PHE   0.022   0.001   PHE A 172 
 TYR   0.014   0.001   TYR A 154 
 ARG   0.004   0.000   ARG B 205 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.8361 (m-40) cc_final: 0.8145 (m-40)
REVERT: A  152 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8572 (mtt)
REVERT: A  161 GLU cc_start: 0.8002 (mp0) cc_final: 0.7778 (mp0)
REVERT: A  223 MET cc_start: 0.8679 (tpp) cc_final: 0.8398 (tpp)
REVERT: A  232 CYS cc_start: 0.8348 (p) cc_final: 0.8104 (p)
REVERT: B   75 GLU cc_start: 0.8407 (tt0) cc_final: 0.7888 (tp30)
REVERT: B  232 CYS cc_start: 0.8470 (p) cc_final: 0.8175 (p)
  outliers start: 16
  outliers final: 6
  residues processed: 85
  average time/residue: 1.0375
  time to fit residues: 94.5493
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain B residue   47 ARG
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   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 185 HIS
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.144723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113667 restraints weight = 7499.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 2.17
r_work: 0.3172 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6903  Z= 0.185
  Angle     :  0.602   8.492   9421  Z= 0.279
  Chirality :  0.043   0.273   1077
  Planarity :  0.004   0.037   1199
  Dihedral  :  8.632  97.999   1255
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 13.47 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.29), residues: 846
  helix:  1.83 (0.31), residues: 314
  sheet: -0.74 (0.36), residues: 178
  loop : -1.19 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 379 
 HIS   0.008   0.001   HIS A 185 
 PHE   0.011   0.001   PHE A 172 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.005   0.000   ARG B 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A    2 ASN cc_start: 0.8377 (m-40) cc_final: 0.8168 (m-40)
REVERT: A   75 GLU cc_start: 0.8205 (tt0) cc_final: 0.7722 (tp30)
REVERT: A  152 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8603 (mtt)
REVERT: A  232 CYS cc_start: 0.8311 (p) cc_final: 0.8079 (p)
REVERT: B   75 GLU cc_start: 0.8317 (tt0) cc_final: 0.7811 (tp30)
REVERT: B  232 CYS cc_start: 0.8473 (p) cc_final: 0.8182 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 92
  average time/residue: 0.8573
  time to fit residues: 85.0222
Evaluate side-chains
  85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain B residue   47 ARG
Chi-restraints excluded: chain B residue   86 CYS
Chi-restraints excluded: chain B residue  200 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.108916 restraints weight = 7462.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.17
r_work: 0.3078 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6903  Z= 0.399
  Angle     :  0.707   9.773   9421  Z= 0.329
  Chirality :  0.047   0.323   1077
  Planarity :  0.005   0.035   1199
  Dihedral  :  8.562  91.906   1255
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.47 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.29), residues: 846
  helix:  1.61 (0.30), residues: 314
  sheet: -0.71 (0.36), residues: 178
  loop : -1.23 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 379 
 HIS   0.008   0.001   HIS B 322 
 PHE   0.015   0.002   PHE A 172 
 TYR   0.016   0.002   TYR A 154 
 ARG   0.004   0.000   ARG A  95 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  232 CYS cc_start: 0.8286 (p) cc_final: 0.7883 (t)
REVERT: A  234 GLU cc_start: 0.8405 (mp0) cc_final: 0.7493 (mp0)
REVERT: B   75 GLU cc_start: 0.8398 (tt0) cc_final: 0.7884 (tp30)
REVERT: B  232 CYS cc_start: 0.8479 (p) cc_final: 0.8193 (p)
  outliers start: 14
  outliers final: 7
  residues processed: 82
  average time/residue: 0.9642
  time to fit residues: 84.7078
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   47 ARG
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  237 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 73 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.144810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113719 restraints weight = 7473.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.17
r_work: 0.3170 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6903  Z= 0.183
  Angle     :  0.611   8.496   9421  Z= 0.283
  Chirality :  0.042   0.262   1077
  Planarity :  0.004   0.037   1199
  Dihedral  :  8.195  94.645   1255
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.71 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 846
  helix:  1.82 (0.31), residues: 316
  sheet: -0.70 (0.36), residues: 178
  loop : -1.16 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 379 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.014   0.001   PHE A 172 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.005   0.000   ARG B 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.8212 (tt0) cc_final: 0.7744 (tp30)
REVERT: A  232 CYS cc_start: 0.8283 (p) cc_final: 0.7926 (t)
REVERT: A  234 GLU cc_start: 0.8261 (mp0) cc_final: 0.7324 (mp0)
REVERT: B   75 GLU cc_start: 0.8326 (tt0) cc_final: 0.7800 (tp30)
REVERT: B  232 CYS cc_start: 0.8494 (p) cc_final: 0.8220 (p)
REVERT: B  341 THR cc_start: 0.8748 (p) cc_final: 0.8413 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 86
  average time/residue: 0.9387
  time to fit residues: 86.9770
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue   47 ARG
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    0.0270
   chunk 81 optimal weight:    0.0770
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0270
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.3054

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
B 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.148755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117051 restraints weight = 7532.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.24
r_work: 0.3215 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6903  Z= 0.155
  Angle     :  0.575   7.547   9421  Z= 0.264
  Chirality :  0.041   0.212   1077
  Planarity :  0.004   0.038   1199
  Dihedral  :  7.483  95.655   1255
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 15.33 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.29), residues: 846
  helix:  1.98 (0.31), residues: 318
  sheet: -0.73 (0.36), residues: 182
  loop : -0.95 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 379 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.014   0.001   PHE A 172 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.004   0.000   ARG A 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A   45 THR cc_start: 0.8594 (m) cc_final: 0.8217 (p)
REVERT: A   61 SER cc_start: 0.8427 (p) cc_final: 0.8219 (t)
REVERT: A   75 GLU cc_start: 0.8167 (tt0) cc_final: 0.7689 (tp30)
REVERT: A  232 CYS cc_start: 0.8243 (p) cc_final: 0.7882 (t)
REVERT: A  234 GLU cc_start: 0.8230 (mp0) cc_final: 0.7244 (mp0)
REVERT: B   75 GLU cc_start: 0.8220 (tt0) cc_final: 0.7744 (tp30)
REVERT: B  173 MET cc_start: 0.8501 (mmt) cc_final: 0.8261 (mmm)
REVERT: B  232 CYS cc_start: 0.8482 (p) cc_final: 0.8187 (p)
REVERT: B  341 THR cc_start: 0.8634 (p) cc_final: 0.8351 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 93
  average time/residue: 0.8953
  time to fit residues: 89.5269
Evaluate side-chains
  85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain B residue   47 ARG
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0670
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.5322

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
A 299 HIS
B  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.112750 restraints weight = 7630.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.22
r_work: 0.3158 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6903  Z= 0.242
  Angle     :  0.633   7.681   9421  Z= 0.292
  Chirality :  0.043   0.240   1077
  Planarity :  0.004   0.036   1199
  Dihedral  :  7.291  89.689   1255
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.10 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 846
  helix:  1.95 (0.31), residues: 318
  sheet: -0.55 (0.36), residues: 178
  loop : -0.96 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 379 
 HIS   0.008   0.001   HIS A 299 
 PHE   0.013   0.001   PHE A 172 
 TYR   0.013   0.001   TYR A 236 
 ARG   0.006   0.000   ARG B 198 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A   45 THR cc_start: 0.8579 (m) cc_final: 0.8132 (p)
REVERT: A   75 GLU cc_start: 0.8191 (tt0) cc_final: 0.7709 (tp30)
REVERT: A  161 GLU cc_start: 0.8311 (mp0) cc_final: 0.6889 (pp20)
REVERT: A  232 CYS cc_start: 0.8210 (p) cc_final: 0.7848 (t)
REVERT: A  234 GLU cc_start: 0.8234 (mp0) cc_final: 0.7252 (mp0)
REVERT: B   75 GLU cc_start: 0.8259 (tt0) cc_final: 0.7786 (tp30)
REVERT: B  341 THR cc_start: 0.8710 (p) cc_final: 0.8420 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 81
  average time/residue: 0.9711
  time to fit residues: 84.2157
Evaluate side-chains
  77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 THR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  182 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   chunk 15 optimal weight:    0.3980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS
A 299 HIS
B  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.146326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.115060 restraints weight = 7619.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.20
r_work: 0.3199 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6903  Z= 0.171
  Angle     :  0.597   7.462   9421  Z= 0.276
  Chirality :  0.042   0.224   1077
  Planarity :  0.004   0.037   1199
  Dihedral  :  7.110  89.031   1255
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 16.56 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.29), residues: 846
  helix:  2.06 (0.30), residues: 318
  sheet: -0.55 (0.36), residues: 178
  loop : -0.91 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 379 
 HIS   0.007   0.001   HIS A 299 
 PHE   0.013   0.001   PHE A 172 
 TYR   0.012   0.001   TYR A 236 
 ARG   0.007   0.000   ARG B 198 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4187.34 seconds
wall clock time: 75 minutes 47.48 seconds (4547.48 seconds total)