Starting phenix.real_space_refine
on Tue Jan 14 12:33:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8urt_42500/01_2025/8urt_42500.cif"
  }
  resolution = 3.8
  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=   0.065
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      4      5.21       5
     S      42      5.16       5
     C    4474      2.51       5
     N     956      2.21       5
     O    1140      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 6622
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
    Chain: "B"
      Number of atoms: 3120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
    Chain: "A"
      Number of atoms: 244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 244
          Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 4}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 136
          Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 4.21, per 1000 atoms: 0.64
  Number of scatterers: 6622
  At special positions: 0
  Unit cell: (89.64, 103.68, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       6     15.00
     Mg      4     11.99
     O    1140      8.00
     N     956      7.00
     C    4474      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 879.4 milliseconds
  

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      79.6% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 14
      removed outlier: 4.757A  pdb=" N   GLY A  11 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LYS A  14 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 30 through 39
      removed outlier: 4.302A  pdb=" N   PHE A  34 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 70
      removed outlier: 4.099A  pdb=" N   PHE A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ILE A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 3.721A  pdb=" N   PHE A  83 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A  86 " --> pdb=" O   TYR A  82 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ARG A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ARG A 105 " --> pdb=" O   MET A 101 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A 106 " --> pdb=" O   HIS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 137
      removed outlier: 3.713A  pdb=" N   GLU A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   THR A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 141 through 165
      removed outlier: 3.905A  pdb=" N   ILE A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   SER A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 193
      removed outlier: 3.793A  pdb=" N   ILE A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 200
    Processing helix  chain 'A' and resid 217 through 250
    Processing helix  chain 'A' and resid 256 through 267
    Processing helix  chain 'A' and resid 268 through 285
      removed outlier: 3.649A  pdb=" N   PHE A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 289
      removed outlier: 3.904A  pdb=" N   ILE A 289 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 286 through 289'
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 322 through 325
    Processing helix  chain 'A' and resid 326 through 341
    Processing helix  chain 'A' and resid 349 through 381
      removed outlier: 4.284A  pdb=" N   TRP A 355 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 15
      removed outlier: 4.753A  pdb=" N   GLY B  11 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LYS B  14 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 30 through 39
      removed outlier: 4.403A  pdb=" N   PHE B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'B' and resid 50 through 70
    Processing helix  chain 'B' and resid 78 through 107
      removed outlier: 3.972A  pdb=" N   TYR B  82 " --> pdb=" O   PRO B  78 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLY B 100 " --> pdb=" O   ASP B  96 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   MET B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 137
      removed outlier: 3.704A  pdb=" N   GLU B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      Proline residue:  B 131  - end of helix
    Processing helix  chain 'B' and resid 141 through 166
      removed outlier: 3.870A  pdb=" N   ILE B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN B 148 " --> pdb=" O   THR B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 193
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 217 through 252
      removed outlier: 4.142A  pdb=" N   ASN B 232 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B 250 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   SER B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 266
      removed outlier: 3.504A  pdb=" N   THR B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 285
    Processing helix  chain 'B' and resid 286 through 289
      removed outlier: 3.984A  pdb=" N   ILE B 289 " --> pdb=" O   PRO B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 289'
    Processing helix  chain 'B' and resid 290 through 315
    Processing helix  chain 'B' and resid 322 through 325
    Processing helix  chain 'B' and resid 326 through 341
      removed outlier: 3.587A  pdb=" N   LEU B 332 " --> pdb=" O   PRO B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 381
      removed outlier: 3.833A  pdb=" N   ILE B 349 " --> pdb=" O   GLN B 345 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL B 350 " --> pdb=" O   LYS B 346 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   SER B 351 " --> pdb=" O   GLY B 347 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B 352 " --> pdb=" O   SER B 348 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204
      removed outlier: 7.146A  pdb=" N   VAL A 215 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 205
      removed outlier: 7.370A  pdb=" N   VAL B 215 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1293 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: 1.74

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 932
        1.31 -     1.43: 2069
        1.43 -     1.56: 3727
        1.56 -     1.68: 22
        1.68 -     1.81: 68
  Bond restraints: 6818
  Sorted by residual:
  bond pdb=" C11 PCW A1003 "
       pdb=" O3  PCW A1003 "
    ideal  model  delta    sigma   weight residual
    1.326  1.421 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C11 PCW A1004 "
       pdb=" O3  PCW A1004 "
    ideal  model  delta    sigma   weight residual
    1.326  1.421 -0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" C11 PCW A1006 "
       pdb=" O3  PCW A1006 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" C11 PCW B 401 "
       pdb=" O3  PCW B 401 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.19e+01
  bond pdb=" C11 PCW A1007 "
       pdb=" O3  PCW A1007 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.19e+01
  ... (remaining 6813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.03: 9144
        5.03 -    10.07: 58
       10.07 -    15.10: 15
       15.10 -    20.14: 9
       20.14 -    25.17: 12
  Bond angle restraints: 9238
  Sorted by residual:
  angle pdb=" C19 PCW A1007 "
        pdb=" C20 PCW A1007 "
        pdb=" C21 PCW A1007 "
      ideal   model   delta    sigma   weight residual
     127.82  152.99  -25.17 3.00e+00 1.11e-01 7.04e+01
  angle pdb=" C19 PCW B 404 "
        pdb=" C20 PCW B 404 "
        pdb=" C21 PCW B 404 "
      ideal   model   delta    sigma   weight residual
     127.82  152.99  -25.17 3.00e+00 1.11e-01 7.04e+01
  angle pdb=" C19 PCW B 401 "
        pdb=" C20 PCW B 401 "
        pdb=" C21 PCW B 401 "
      ideal   model   delta    sigma   weight residual
     127.82  152.75  -24.93 3.00e+00 1.11e-01 6.91e+01
  angle pdb=" C19 PCW A1004 "
        pdb=" C20 PCW A1004 "
        pdb=" C21 PCW A1004 "
      ideal   model   delta    sigma   weight residual
     127.82  152.71  -24.89 3.00e+00 1.11e-01 6.89e+01
  angle pdb=" C19 PCW A1006 "
        pdb=" C20 PCW A1006 "
        pdb=" C21 PCW A1006 "
      ideal   model   delta    sigma   weight residual
     127.82  152.58  -24.76 3.00e+00 1.11e-01 6.81e+01
  ... (remaining 9233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.25: 3634
       31.25 -    62.50: 279
       62.50 -    93.75: 34
       93.75 -   125.00: 2
      125.00 -   156.25: 5
  Dihedral angle restraints: 3954
    sinusoidal: 1676
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" N   PCW A1003 "
           pdb=" C4  PCW A1003 "
           pdb=" C5  PCW A1003 "
           pdb=" O4P PCW A1003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  137.09  156.25     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" N   PCW B 404 "
           pdb=" C4  PCW B 404 "
           pdb=" C5  PCW B 404 "
           pdb=" O4P PCW B 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  148.19  145.15     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" N   PCW B 401 "
           pdb=" C4  PCW B 401 "
           pdb=" C5  PCW B 401 "
           pdb=" O4P PCW B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  158.33  135.01     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 3951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 755
       0.044 -    0.088: 199
       0.088 -    0.133: 38
       0.133 -    0.177: 0
       0.177 -    0.221: 6
  Chirality restraints: 998
  Sorted by residual:
  chirality pdb=" C2  PCW A1003 "
            pdb=" C1  PCW A1003 "
            pdb=" C3  PCW A1003 "
            pdb=" O2  PCW A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" C2  PCW B 404 "
            pdb=" C1  PCW B 404 "
            pdb=" C3  PCW B 404 "
            pdb=" O2  PCW B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" C2  PCW A1006 "
            pdb=" C1  PCW A1006 "
            pdb=" C3  PCW A1006 "
            pdb=" O2  PCW A1006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 995 not shown)

  Planarity restraints: 1102
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  47 "   -0.037 5.00e-02 4.00e+02   5.72e-02 5.23e+00
        pdb=" N   PRO A  48 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 160 "    0.012 2.00e-02 2.50e+03   8.36e-03 1.75e+00
        pdb=" CG  TRP B 160 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 160 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 160 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 160 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 160 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 160 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 169 "    0.008 2.00e-02 2.50e+03   8.93e-03 1.60e+00
        pdb=" CG  TYR A 169 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 169 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 169 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 169 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 169 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 169 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 169 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1099 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 35
        2.58 -     3.16: 5157
        3.16 -     3.74: 9936
        3.74 -     4.32: 13508
        4.32 -     4.90: 23579
  Nonbonded interactions: 52215
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  92 "
            pdb="MG    MG B 403 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MG    MG A1001 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" OD2 ASP B 117 "
            pdb="MG    MG B 402 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" OD2 ASP A  96 "
            pdb="MG    MG A1002 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O   PRO B  78 "
            pdb=" OG1 THR B  81 "
     model   vdw
     2.138 3.040
  ... (remaining 52210 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 388 or resid 1002 or resid 1004 through 1005))
  selection = (chain 'B' and (resid 1 through 388 or resid 402 or resid 404 through 405))
}

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:             1.000
  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:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.320
  Find NCS groups from input model:        0.270
  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:3.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
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      :  0.008   0.095   6818  Z= 0.504
  Angle     :  1.441  25.171   9238  Z= 0.529
  Chirality :  0.041   0.221    998
  Planarity :  0.004   0.057   1102
  Dihedral  : 21.441 156.245   2494
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.59 %
    Favored  : 78.51 %
  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:  2.20 (0.31), residues: 770
  helix:  2.48 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.014   0.001   PHE B 206 
 TYR   0.022   0.001   TYR A 169 
 ARG   0.001   0.000   ARG A 105 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A  128 SER cc_start: 0.8486 (t) cc_final: 0.8104 (p)
REVERT: A  326 LEU cc_start: 0.7443 (mt) cc_final: 0.7204 (mt)
REVERT: B   41 ILE cc_start: 0.7719 (tt) cc_final: 0.7284 (mm)
REVERT: B  127 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6346 (mp)
REVERT: B  128 SER cc_start: 0.8467 (t) cc_final: 0.8047 (p)
REVERT: B  168 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6178 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1293
  time to fit residues: 15.9156
Evaluate side-chains
  80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  296 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  174 CYS
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  290 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0040
   chunk 19 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0770
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.1908

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.138207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.101055 restraints weight = 67884.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.102991 restraints weight = 44484.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.102096 restraints weight = 35839.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.0697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6818  Z= 0.135
  Angle     :  0.492   6.422   9238  Z= 0.237
  Chirality :  0.037   0.120    998
  Planarity :  0.004   0.055   1102
  Dihedral  : 20.062 137.843   1145
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.13 %
    Favored  : 79.82 %
  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:  2.50 (0.31), residues: 770
  helix:  2.80 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.30 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS B 164 
 PHE   0.011   0.001   PHE B 206 
 TYR   0.009   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 242 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A   99 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6835 (p0)
REVERT: A  193 TYR cc_start: 0.8693 (m-80) cc_final: 0.8424 (m-80)
REVERT: B    7 GLN cc_start: 0.7149 (tp40) cc_final: 0.6543 (pt0)
REVERT: B   41 ILE cc_start: 0.8111 (tt) cc_final: 0.7586 (mm)
REVERT: B  388 LYS cc_start: 0.6282 (OUTLIER) cc_final: 0.4710 (tptt)
  outliers start: 14
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1321
  time to fit residues: 17.1001
Evaluate side-chains
  80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0070
   chunk 57 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
B 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.141628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.099473 restraints weight = 66322.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.101096 restraints weight = 39575.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.100742 restraints weight = 35788.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6818  Z= 0.175
  Angle     :  0.495   6.130   9238  Z= 0.241
  Chirality :  0.038   0.119    998
  Planarity :  0.004   0.050   1102
  Dihedral  : 18.237 133.297   1136
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.69 %
    Favored  : 79.53 %
  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:  2.53 (0.31), residues: 770
  helix:  2.81 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.26 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A 275 
 TYR   0.015   0.001   TYR A 169 
 ARG   0.001   0.000   ARG A  79 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A   99 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6737 (p0)
REVERT: A  193 TYR cc_start: 0.8701 (m-80) cc_final: 0.8472 (m-80)
REVERT: B    7 GLN cc_start: 0.7113 (tp40) cc_final: 0.6527 (pt0)
REVERT: B   41 ILE cc_start: 0.7972 (tt) cc_final: 0.7452 (mm)
REVERT: B  127 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6775 (mp)
REVERT: B  157 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8204 (mp)
REVERT: B  388 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.4468 (tptt)
  outliers start: 19
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1525
  time to fit residues: 19.0166
Evaluate side-chains
  86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.141263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.099547 restraints weight = 67014.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.101385 restraints weight = 38203.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.100893 restraints weight = 33710.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6818  Z= 0.180
  Angle     :  0.492   6.075   9238  Z= 0.240
  Chirality :  0.038   0.119    998
  Planarity :  0.004   0.047   1102
  Dihedral  : 16.685 125.883   1135
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.25 %
    Favored  : 79.82 %
  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:  2.54 (0.31), residues: 770
  helix:  2.80 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.22 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A 275 
 TYR   0.014   0.001   TYR A 169 
 ARG   0.001   0.000   ARG B  23 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7260 (mtt180)
REVERT: A   99 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6655 (p0)
REVERT: A  193 TYR cc_start: 0.8703 (m-80) cc_final: 0.8488 (m-80)
REVERT: B    7 GLN cc_start: 0.7053 (tp40) cc_final: 0.6377 (pt0)
REVERT: B   41 ILE cc_start: 0.7936 (tt) cc_final: 0.7421 (mm)
REVERT: B  127 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6812 (mp)
REVERT: B  157 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8108 (mp)
REVERT: B  383 TYR cc_start: 0.8120 (m-80) cc_final: 0.7897 (m-80)
REVERT: B  388 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.4841 (ttpp)
  outliers start: 20
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1792
  time to fit residues: 21.9255
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  388 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.139786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.097685 restraints weight = 65528.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.099149 restraints weight = 40957.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.099551 restraints weight = 31978.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6818  Z= 0.216
  Angle     :  0.513   6.118   9238  Z= 0.252
  Chirality :  0.039   0.121    998
  Planarity :  0.004   0.046   1102
  Dihedral  : 15.468 120.381   1135
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.54 %
    Favored  : 79.68 %
  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:  2.44 (0.31), residues: 770
  helix:  2.72 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.25 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 160 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.012   0.001   PHE B 275 
 TYR   0.014   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 307 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A   79 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7370 (mtt180)
REVERT: A   99 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6737 (p0)
REVERT: A  109 GLN cc_start: 0.7307 (mt0) cc_final: 0.6745 (mp10)
REVERT: A  193 TYR cc_start: 0.8730 (m-80) cc_final: 0.8509 (m-80)
REVERT: B    7 GLN cc_start: 0.7182 (tp40) cc_final: 0.6616 (pt0)
REVERT: B   41 ILE cc_start: 0.8029 (tt) cc_final: 0.7503 (mm)
REVERT: B  104 ARG cc_start: 0.6463 (mmt90) cc_final: 0.6053 (mtm110)
REVERT: B  127 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7093 (mp)
REVERT: B  157 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8131 (mp)
REVERT: B  383 TYR cc_start: 0.8304 (m-80) cc_final: 0.8020 (m-80)
  outliers start: 19
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1677
  time to fit residues: 20.0626
Evaluate side-chains
  88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0770
   overall best weight:    0.6138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.134473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.094737 restraints weight = 67283.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.096415 restraints weight = 44409.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.096063 restraints weight = 39329.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6818  Z= 0.178
  Angle     :  0.495   6.903   9238  Z= 0.240
  Chirality :  0.038   0.117    998
  Planarity :  0.004   0.045   1102
  Dihedral  : 14.760 116.249   1135
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.27 %
    Favored  : 78.95 %
  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:  2.53 (0.31), residues: 770
  helix:  2.79 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.25 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 160 
 HIS   0.002   0.001   HIS A 164 
 PHE   0.011   0.001   PHE A 275 
 TYR   0.013   0.001   TYR A 169 
 ARG   0.000   0.000   ARG B  36 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7213 (tp40) cc_final: 0.6539 (tp40)
REVERT: A   79 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7352 (mtt180)
REVERT: A   99 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6745 (p0)
REVERT: A  349 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8397 (mm)
REVERT: B    7 GLN cc_start: 0.7150 (tp40) cc_final: 0.6462 (pt0)
REVERT: B   41 ILE cc_start: 0.7983 (tt) cc_final: 0.7468 (mm)
REVERT: B  104 ARG cc_start: 0.6228 (mmt90) cc_final: 0.5795 (mtm110)
REVERT: B  127 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7016 (mp)
REVERT: B  383 TYR cc_start: 0.8236 (m-80) cc_final: 0.7909 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 86
  average time/residue: 0.1710
  time to fit residues: 20.8037
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   chunk 53 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 44 optimal weight:    0.0270
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4016

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.137187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.098205 restraints weight = 67821.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.099861 restraints weight = 44924.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.099603 restraints weight = 39113.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6818  Z= 0.150
  Angle     :  0.477   6.502   9238  Z= 0.231
  Chirality :  0.038   0.127    998
  Planarity :  0.004   0.044   1102
  Dihedral  : 13.829 109.518   1135
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.98 %
    Favored  : 79.39 %
  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:  2.72 (0.31), residues: 770
  helix:  2.95 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.19 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 118 
 PHE   0.010   0.001   PHE B 206 
 TYR   0.013   0.001   TYR A 169 
 ARG   0.001   0.000   ARG A 307 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7084 (tp40) cc_final: 0.6414 (tp40)
REVERT: A   79 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7254 (mtt180)
REVERT: A   99 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6956 (p0)
REVERT: A  349 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8361 (mm)
REVERT: B    7 GLN cc_start: 0.6987 (tp40) cc_final: 0.6296 (pt0)
REVERT: B   41 ILE cc_start: 0.8015 (tt) cc_final: 0.7501 (mm)
REVERT: B  383 TYR cc_start: 0.8185 (m-80) cc_final: 0.7864 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 85
  average time/residue: 0.1508
  time to fit residues: 18.4078
Evaluate side-chains
  85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 70 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0040
   overall best weight:    0.4392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.144032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.101763 restraints weight = 66643.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.104177 restraints weight = 39732.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.103557 restraints weight = 33636.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6818  Z= 0.157
  Angle     :  0.484   6.752   9238  Z= 0.234
  Chirality :  0.038   0.133    998
  Planarity :  0.003   0.043   1102
  Dihedral  : 13.532 105.676   1133
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.42 %
    Favored  : 79.09 %
  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:  2.73 (0.31), residues: 770
  helix:  2.95 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.16 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 160 
 HIS   0.002   0.001   HIS B 164 
 PHE   0.010   0.001   PHE B 206 
 TYR   0.013   0.001   TYR A 169 
 ARG   0.001   0.000   ARG A 242 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7066 (tp40) cc_final: 0.6394 (tp40)
REVERT: A   79 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7283 (mtt180)
REVERT: A   99 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6865 (p0)
REVERT: A  349 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: B    7 GLN cc_start: 0.6895 (tp40) cc_final: 0.6193 (pt0)
REVERT: B   41 ILE cc_start: 0.7987 (tt) cc_final: 0.7484 (mm)
REVERT: B  383 TYR cc_start: 0.8132 (m-80) cc_final: 0.7778 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1527
  time to fit residues: 18.5364
Evaluate side-chains
  84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.133659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.093524 restraints weight = 66526.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.095650 restraints weight = 43655.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.094759 restraints weight = 36650.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6818  Z= 0.223
  Angle     :  0.523   6.769   9238  Z= 0.255
  Chirality :  0.040   0.144    998
  Planarity :  0.004   0.043   1102
  Dihedral  : 13.555 101.969   1133
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.57 %
    Favored  : 79.09 %
  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:  2.53 (0.31), residues: 770
  helix:  2.75 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.13 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A 275 
 TYR   0.014   0.001   TYR B 274 
 ARG   0.001   0.000   ARG B  32 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7100 (tp40) cc_final: 0.6269 (tp40)
REVERT: A   79 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7474 (mtt180)
REVERT: A   99 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7051 (p0)
REVERT: A  349 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8537 (mm)
REVERT: B   41 ILE cc_start: 0.7992 (tt) cc_final: 0.7458 (mm)
REVERT: B  104 ARG cc_start: 0.6353 (mmt90) cc_final: 0.5909 (mtm110)
REVERT: B  383 TYR cc_start: 0.8204 (m-80) cc_final: 0.7897 (m-80)
  outliers start: 16
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1620
  time to fit residues: 19.2498
Evaluate side-chains
  83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.133933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.094477 restraints weight = 67889.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.096164 restraints weight = 46754.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.095597 restraints weight = 39569.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6818  Z= 0.205
  Angle     :  0.515   6.982   9238  Z= 0.252
  Chirality :  0.039   0.163    998
  Planarity :  0.004   0.043   1102
  Dihedral  : 13.321  98.503   1133
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.71 %
    Favored  : 79.09 %
  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:  2.49 (0.31), residues: 770
  helix:  2.74 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.18 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A 275 
 TYR   0.013   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 242 

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

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

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1540 Ramachandran restraints generated.
    770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7093 (tp40) cc_final: 0.6243 (tp40)
REVERT: A   79 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7332 (mtt180)
REVERT: A   99 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6998 (p0)
REVERT: A  109 GLN cc_start: 0.7261 (mt0) cc_final: 0.6838 (mp10)
REVERT: A  349 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8518 (mm)
REVERT: B   41 ILE cc_start: 0.8024 (tt) cc_final: 0.7491 (mm)
REVERT: B  104 ARG cc_start: 0.6384 (mmt90) cc_final: 0.5922 (mtm110)
REVERT: B  383 TYR cc_start: 0.8153 (m-80) cc_final: 0.7870 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1653
  time to fit residues: 19.3284
Evaluate side-chains
  84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ARG
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  351 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0020
   chunk 11 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.137063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.098463 restraints weight = 65882.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.100466 restraints weight = 44015.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.099606 restraints weight = 37511.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6818  Z= 0.154
  Angle     :  0.486   6.897   9238  Z= 0.236
  Chirality :  0.038   0.147    998
  Planarity :  0.004   0.043   1102
  Dihedral  : 12.639  93.821   1133
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.86 %
    Favored  : 78.95 %
  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:  2.70 (0.31), residues: 770
  helix:  2.92 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.15 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 160 
 HIS   0.002   0.001   HIS B 164 
 PHE   0.017   0.001   PHE B  34 
 TYR   0.012   0.001   TYR A 169 
 ARG   0.000   0.000   ARG A 307 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1864.60 seconds
wall clock time: 35 minutes 14.45 seconds (2114.45 seconds total)