Starting phenix.real_space_refine
on Tue May 13 02:44:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7v_15903/05_2025/8b7v_15903.cif"
  }
  resolution = 3.0
  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=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6330      2.51       5
     N    1713      2.21       5
     O    1965      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10050
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
    Chain: "B"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
    Chain: "C"
      Number of atoms: 3350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 421, 3350
          Classifications: {'peptide': 421}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 412}
  Time building chain proxies: 5.54, per 1000 atoms: 0.55
  Number of scatterers: 10050
  At special positions: 0
  Unit cell: (97.11, 96.28, 76.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1965      8.00
     N    1713      7.00
     C    6330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  38 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  38 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.13
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2238

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      4.0% alpha, 57.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 238 through 240
      No H-bonds generated for 'chain 'A' and resid 238 through 240'
    Processing helix  chain 'A' and resid 397 through 401
    Processing helix  chain 'B' and resid 113 through 116
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 238 through 240
      No H-bonds generated for 'chain 'B' and resid 238 through 240'
    Processing helix  chain 'B' and resid 397 through 401
    Processing helix  chain 'C' and resid 113 through 116
    Processing helix  chain 'C' and resid 159 through 163
      removed outlier: 3.566A  pdb=" N   ASP C 162 " --> pdb=" O   ASN C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 240
      No H-bonds generated for 'chain 'C' and resid 238 through 240'
    Processing helix  chain 'C' and resid 397 through 401
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14
      removed outlier: 4.015A  pdb=" N   LEU A  46 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR A  62 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   PHE A  58 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LYS A  52 " --> pdb=" O   LYS A  56 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LYS A  56 " --> pdb=" O   LYS A  52 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA A  65 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   PHE A  81 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   LEU A 139 " --> pdb=" O   ASN A 131 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 142 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLY A 150 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   ASN A 165 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA A 168 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A 178 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   LEU A 187 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   GLU A 180 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   GLY A 185 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP A 213 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112
      removed outlier: 3.516A  pdb=" N   TRP A 120 " --> pdb=" O   HIS A 110 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL A 112 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   TYR A 118 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254
    Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14
      removed outlier: 3.968A  pdb=" N   LEU B  46 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B  62 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   PHE B  58 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   LYS B  52 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LYS B  56 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA B  65 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   PHE B  81 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 11.618A  pdb=" N   GLY B 124 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 10.464A  pdb=" N   SER B 147 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   GLY B 126 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   ARG B 145 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   GLY B 128 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ALA B 143 " --> pdb=" O   GLY B 128 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   GLU B 130 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   LEU B 141 " --> pdb=" O   GLU B 130 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA B 142 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLY B 150 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ASN B 165 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA B 168 " --> pdb=" O   ASN B 197 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   LEU B 187 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP B 213 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   MET B 320 " --> pdb=" O   TRP B 316 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112
      removed outlier: 6.898A  pdb=" N   HIS B 110 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254
    Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378
    Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 204
      removed outlier: 4.081A  pdb=" N   ALA C 142 " --> pdb=" O   ASP C 173 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY C 150 " --> pdb=" O   ASN C 165 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   ASN C 165 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA C 168 " --> pdb=" O   ASN C 197 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   LEU C 187 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLU C 180 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   GLY C 185 " --> pdb=" O   GLU C 180 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TRP C 213 " --> pdb=" O   THR C 236 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TRP C 284 " --> pdb=" O   MET C 280 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET C 320 " --> pdb=" O   TRP C 316 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU C  46 " --> pdb=" O   THR C  62 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   THR C  62 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   PHE C  58 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LYS C  52 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LYS C  56 " --> pdb=" O   LYS C  52 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   SER C  57 " --> pdb=" O   GLY C  88 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   GLY C  88 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TYR C  59 " --> pdb=" O   VAL C  86 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL C  86 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ASP C  61 " --> pdb=" O   ALA C  84 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA C  84 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   ASN C  63 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   LEU C 139 " --> pdb=" O   ASN C 131 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112
      removed outlier: 6.659A  pdb=" N   VAL C 112 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   TYR C 118 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254
    Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379
      removed outlier: 4.020A  pdb=" N   LYS C 392 " --> pdb=" O   ASP C 379 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1551 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: 3.11

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2204
        1.34 -     1.46: 3960
        1.46 -     1.58: 4087
        1.58 -     1.71: 0
        1.71 -     1.83: 78
  Bond restraints: 10329
  Sorted by residual:
  bond pdb=" CD  ARG B 335 "
       pdb=" NE  ARG B 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.510 -0.052 1.40e-02 5.10e+03 1.39e+01
  bond pdb=" CD  ARG C 335 "
       pdb=" NE  ARG C 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.510 -0.052 1.40e-02 5.10e+03 1.36e+01
  bond pdb=" CD  ARG A 335 "
       pdb=" NE  ARG A 335 "
    ideal  model  delta    sigma   weight residual
    1.458  1.509 -0.051 1.40e-02 5.10e+03 1.31e+01
  bond pdb=" CE1 HIS B 275 "
       pdb=" NE2 HIS B 275 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.30e+01
  bond pdb=" CE1 HIS C 275 "
       pdb=" NE2 HIS C 275 "
    ideal  model  delta    sigma   weight residual
    1.321  1.357 -0.036 1.00e-02 1.00e+04 1.27e+01
  ... (remaining 10324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 10932
        2.09 -     4.18: 2642
        4.18 -     6.28: 391
        6.28 -     8.37: 43
        8.37 -    10.46: 2
  Bond angle restraints: 14010
  Sorted by residual:
  angle pdb=" CA  ARG C 360 "
        pdb=" C   ARG C 360 "
        pdb=" N   PRO C 361 "
      ideal   model   delta    sigma   weight residual
     117.68  126.03   -8.35 7.10e-01 1.98e+00 1.38e+02
  angle pdb=" CA  THR B 317 "
        pdb=" C   THR B 317 "
        pdb=" N   PRO B 318 "
      ideal   model   delta    sigma   weight residual
     117.96  125.95   -7.99 8.10e-01 1.52e+00 9.72e+01
  angle pdb=" CA  THR C 317 "
        pdb=" C   THR C 317 "
        pdb=" N   PRO C 318 "
      ideal   model   delta    sigma   weight residual
     117.96  125.52   -7.56 8.10e-01 1.52e+00 8.71e+01
  angle pdb=" CA  ARG B 360 "
        pdb=" C   ARG B 360 "
        pdb=" N   PRO B 361 "
      ideal   model   delta    sigma   weight residual
     117.95  125.05   -7.10 7.70e-01 1.69e+00 8.50e+01
  angle pdb=" CA  ASP A 211 "
        pdb=" CB  ASP A 211 "
        pdb=" CG  ASP A 211 "
      ideal   model   delta    sigma   weight residual
     112.60  119.94   -7.34 1.00e+00 1.00e+00 5.39e+01
  ... (remaining 14005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.77: 5385
       18.77 -    37.54: 313
       37.54 -    56.32: 60
       56.32 -    75.09: 58
       75.09 -    93.86: 22
  Dihedral angle restraints: 5838
    sinusoidal: 2274
      harmonic: 3564
  Sorted by residual:
  dihedral pdb=" N   GLN B  70 "
           pdb=" C   GLN B  70 "
           pdb=" CA  GLN B  70 "
           pdb=" CB  GLN B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.61  -14.81     0      2.50e+00 1.60e-01 3.51e+01
  dihedral pdb=" CA  TYR B  32 "
           pdb=" C   TYR B  32 "
           pdb=" N   ARG B  33 "
           pdb=" CA  ARG B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.66  -29.34     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" C   GLN B  70 "
           pdb=" N   GLN B  70 "
           pdb=" CA  GLN B  70 "
           pdb=" CB  GLN B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.11   14.51     0      2.50e+00 1.60e-01 3.37e+01
  ... (remaining 5835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1021
       0.116 -    0.232: 284
       0.232 -    0.348: 53
       0.348 -    0.464: 7
       0.464 -    0.580: 3
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" CA  GLN B  70 "
            pdb=" N   GLN B  70 "
            pdb=" C   GLN B  70 "
            pdb=" CB  GLN B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.93    0.58 2.00e-01 2.50e+01 8.40e+00
  chirality pdb=" CA  GLN A  70 "
            pdb=" N   GLN A  70 "
            pdb=" C   GLN A  70 "
            pdb=" CB  GLN A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.63e+00
  chirality pdb=" CA  GLN C  70 "
            pdb=" N   GLN C  70 "
            pdb=" C   GLN C  70 "
            pdb=" CB  GLN C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.84e+00
  ... (remaining 1365 not shown)

  Planarity restraints: 1854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 118 "   -0.202 2.00e-02 2.50e+03   1.21e-01 2.91e+02
        pdb=" CG  TYR C 118 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 118 "    0.078 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 118 "    0.087 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 118 "    0.075 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 118 "    0.089 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 118 "    0.043 2.00e-02 2.50e+03
        pdb=" OH  TYR C 118 "   -0.211 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 118 "   -0.164 2.00e-02 2.50e+03   9.65e-02 1.86e+02
        pdb=" CG  TYR A 118 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 118 "    0.073 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 118 "    0.059 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 118 "    0.066 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 118 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 118 "    0.036 2.00e-02 2.50e+03
        pdb=" OH  TYR A 118 "   -0.168 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  32 "    0.125 2.00e-02 2.50e+03   7.29e-02 1.06e+02
        pdb=" CG  TYR A  32 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  32 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  32 "   -0.051 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  32 "   -0.050 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  32 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  32 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR A  32 "    0.124 2.00e-02 2.50e+03
  ... (remaining 1851 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3752
        2.91 -     3.41: 8290
        3.41 -     3.90: 17791
        3.90 -     4.40: 19949
        4.40 -     4.90: 35305
  Nonbonded interactions: 85087
  Sorted by model distance:
  nonbonded pdb=" N   THR B 317 "
            pdb=" O   THR B 317 "
     model   vdw
     2.409 2.496
  nonbonded pdb=" N   THR C 317 "
            pdb=" O   THR C 317 "
     model   vdw
     2.425 2.496
  nonbonded pdb=" N   ARG C 360 "
            pdb=" O   ARG C 360 "
     model   vdw
     2.449 2.496
  nonbonded pdb=" N   THR A 317 "
            pdb=" O   THR A 317 "
     model   vdw
     2.465 2.496
  nonbonded pdb=" N   ARG B 360 "
            pdb=" O   ARG B 360 "
     model   vdw
     2.488 2.496
  ... (remaining 85082 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.080
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.050
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  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:12.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
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      :  0.015   0.052  10332  Z= 0.848
  Angle     :  1.804  10.461  14016  Z= 1.245
  Chirality :  0.114   0.580   1368
  Planarity :  0.019   0.276   1854
  Dihedral  : 15.921  93.858   3591
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 0.05
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  2.63 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  5.29 %
    Favored  : 92.94 %
  Cbeta Deviations :  0.71 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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 (0.21), residues: 1257
  helix: -4.93 (0.16), residues: 18
  sheet:  1.57 (0.19), residues: 612
  loop : -1.85 (0.20), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.100   0.015   TRP A  51 
 HIS   0.012   0.003   HIS A   4 
 PHE   0.076   0.011   PHE C 254 
 TYR   0.211   0.022   TYR C 118 
 ARG   0.042   0.005   ARG B  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14269 (  560)
  hydrogen bonds       : angle       7.62839 ( 1551)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       1.38489 (    6)
  covalent geometry    : bond        0.01474 (10329)
  covalent geometry    : angle       1.80416 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 2
  residues processed: 146
  average time/residue: 1.4557
  time to fit residues: 225.5797
Evaluate side-chains
  76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain B residue  420 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 64 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A   4 HIS
A  70 GLN
A 349 GLN
B   4 HIS
B  70 GLN
B  90 ASN
C   4 HIS
C  70 GLN
C 159 ASN
C 165 ASN
C 341 ASN
C 386 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.070914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.057969 restraints weight = 20021.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.06
r_work: 0.2614 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10332  Z= 0.185
  Angle     :  0.638   5.616  14016  Z= 0.363
  Chirality :  0.046   0.148   1368
  Planarity :  0.004   0.064   1854
  Dihedral  :  6.309  61.099   1381
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  8.53 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.24 (0.21), residues: 1257
  helix: -4.98 (0.13), residues: 18
  sheet:  1.24 (0.19), residues: 600
  loop : -1.50 (0.20), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 120 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  58 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.008   0.001   ARG C 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  560)
  hydrogen bonds       : angle       5.69643 ( 1551)
  SS BOND              : bond        0.01542 (    3)
  SS BOND              : angle       3.34440 (    6)
  covalent geometry    : bond        0.00403 (10329)
  covalent geometry    : angle       0.63392 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7724 (mt-10)
REVERT: A   53 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: B   39 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8314 (pm20)
REVERT: B   49 GLU cc_start: 0.8986 (tt0) cc_final: 0.8677 (tm-30)
REVERT: B   53 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: B  148 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: B  179 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8528 (mtm)
REVERT: B  188 GLU cc_start: 0.9090 (tt0) cc_final: 0.8886 (tt0)
  outliers start: 27
  outliers final: 0
  residues processed: 89
  average time/residue: 1.3964
  time to fit residues: 133.6415
Evaluate side-chains
  57 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 106 optimal weight:    9.9990
   chunk 77 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 159 ASN
C 416 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.068675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.055670 restraints weight = 20527.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 3.09
r_work: 0.2569 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10332  Z= 0.211
  Angle     :  0.601   8.334  14016  Z= 0.337
  Chirality :  0.045   0.150   1368
  Planarity :  0.004   0.063   1854
  Dihedral  :  5.614  24.977   1377
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.91 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.71 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.42 (0.21), residues: 1257
  helix: -5.05 (0.12), residues: 18
  sheet:  0.95 (0.20), residues: 606
  loop : -1.45 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 120 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.009   0.001   PHE B  23 
 TYR   0.016   0.001   TYR A 343 
 ARG   0.004   0.001   ARG C 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03288 (  560)
  hydrogen bonds       : angle       5.46008 ( 1551)
  SS BOND              : bond        0.01150 (    3)
  SS BOND              : angle       2.22760 (    6)
  covalent geometry    : bond        0.00469 (10329)
  covalent geometry    : angle       0.59958 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7885 (mt-10)
REVERT: A   53 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: B   39 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8564 (pm20)
REVERT: B   49 GLU cc_start: 0.9005 (tt0) cc_final: 0.8636 (tm-30)
REVERT: B   53 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: B  179 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8659 (mpp)
REVERT: B  188 GLU cc_start: 0.9063 (tt0) cc_final: 0.8837 (tt0)
REVERT: C   53 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7990 (mp0)
  outliers start: 18
  outliers final: 1
  residues processed: 80
  average time/residue: 1.4426
  time to fit residues: 123.1866
Evaluate side-chains
  65 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   53 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 60 optimal weight:   30.0000
   chunk 20 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 9 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
B 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.067806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.054906 restraints weight = 20388.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 3.07
r_work: 0.2554 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10332  Z= 0.225
  Angle     :  0.586   7.211  14016  Z= 0.328
  Chirality :  0.044   0.144   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.426  19.913   1377
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.91 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.69 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.53 (0.21), residues: 1257
  helix: -5.07 (0.11), residues: 18
  sheet:  0.82 (0.20), residues: 606
  loop : -1.45 (0.20), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.008   0.001   PHE B  23 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.006   0.001   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03160 (  560)
  hydrogen bonds       : angle       5.38768 ( 1551)
  SS BOND              : bond        0.00557 (    3)
  SS BOND              : angle       2.47563 (    6)
  covalent geometry    : bond        0.00503 (10329)
  covalent geometry    : angle       0.58427 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.183 
Fit side-chains
REVERT: A   37 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: A   53 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7996 (tm-30)
REVERT: A   78 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8995 (m-30)
REVERT: B   39 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8643 (pm20)
REVERT: B   49 GLU cc_start: 0.9007 (tt0) cc_final: 0.8665 (tm-30)
REVERT: B   53 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8012 (tm-30)
REVERT: B  188 GLU cc_start: 0.9071 (tt0) cc_final: 0.8841 (tt0)
REVERT: C   53 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8028 (mp0)
REVERT: C  100 ILE cc_start: 0.9119 (tp) cc_final: 0.8771 (pp)
REVERT: C  148 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7645 (mt-10)
  outliers start: 11
  outliers final: 0
  residues processed: 73
  average time/residue: 1.4702
  time to fit residues: 114.7826
Evaluate side-chains
  63 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain C residue   53 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 106 optimal weight:   20.0000
   chunk 35 optimal weight:   20.0000
   chunk 111 optimal weight:    9.9990
   chunk 83 optimal weight:   30.0000
   chunk 56 optimal weight:    9.9990
   chunk 113 optimal weight:    9.9990
   overall best weight:    8.3990

-------------------------------------------------------------------------------
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 = 0.2954 r_free = 0.2954 target = 0.067443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.054504 restraints weight = 20388.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.2692 rms_B_bonded: 3.07
r_work: 0.2547 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10332  Z= 0.235
  Angle     :  0.594   8.029  14016  Z= 0.331
  Chirality :  0.044   0.141   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.424  24.956   1377
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.15 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.88 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.55 (0.22), residues: 1257
  helix: -5.07 (0.11), residues: 18
  sheet:  0.78 (0.20), residues: 600
  loop : -1.41 (0.21), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.007   0.001   PHE A  58 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.005   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  560)
  hydrogen bonds       : angle       5.35441 ( 1551)
  SS BOND              : bond        0.00485 (    3)
  SS BOND              : angle       4.54519 (    6)
  covalent geometry    : bond        0.00525 (10329)
  covalent geometry    : angle       0.58654 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A   78 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8973 (m-30)
REVERT: A  130 GLU cc_start: 0.9027 (tt0) cc_final: 0.8762 (pt0)
REVERT: A  195 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8078 (ptm-80)
REVERT: A  417 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8636 (ppp)
REVERT: B   39 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8511 (pm20)
REVERT: B   49 GLU cc_start: 0.9006 (tt0) cc_final: 0.8669 (tm-30)
REVERT: B   53 GLU cc_start: 0.8408 (tm-30) cc_final: 0.7980 (tm-30)
REVERT: B  148 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: B  179 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (mtm)
REVERT: B  188 GLU cc_start: 0.9076 (tt0) cc_final: 0.8839 (tt0)
REVERT: C  100 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8766 (pp)
REVERT: C  130 GLU cc_start: 0.8983 (tt0) cc_final: 0.8582 (pt0)
REVERT: C  148 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7593 (mt-10)
  outliers start: 17
  outliers final: 3
  residues processed: 74
  average time/residue: 1.4554
  time to fit residues: 115.3275
Evaluate side-chains
  70 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    0.0770
   chunk 44 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 110 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 99 optimal weight:   40.0000
   chunk 55 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    4.4146

-------------------------------------------------------------------------------
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 = 0.2985 r_free = 0.2985 target = 0.069044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.056043 restraints weight = 20343.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 3.08
r_work: 0.2570 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10332  Z= 0.139
  Angle     :  0.543   6.500  14016  Z= 0.304
  Chirality :  0.043   0.138   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.158  20.944   1377
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.75 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.27 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.68 (0.20), residues: 588
  loop : -1.27 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.005   0.001   PHE B  58 
 TYR   0.012   0.001   TYR C 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02675 (  560)
  hydrogen bonds       : angle       5.17601 ( 1551)
  SS BOND              : bond        0.00475 (    3)
  SS BOND              : angle       3.20263 (    6)
  covalent geometry    : bond        0.00305 (10329)
  covalent geometry    : angle       0.53911 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: A  130 GLU cc_start: 0.8973 (tt0) cc_final: 0.8758 (pt0)
REVERT: A  195 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9006 (tt0) cc_final: 0.8634 (tm-30)
REVERT: B   53 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: B   75 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: B   93 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7420 (pm20)
REVERT: B  148 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: B  179 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8691 (mpp)
REVERT: B  188 GLU cc_start: 0.9067 (tt0) cc_final: 0.8816 (tt0)
REVERT: C   53 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (mp0)
REVERT: C  100 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8778 (pp)
REVERT: C  130 GLU cc_start: 0.8955 (tt0) cc_final: 0.8562 (pt0)
REVERT: C  148 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7566 (mt-10)
  outliers start: 17
  outliers final: 2
  residues processed: 81
  average time/residue: 1.4333
  time to fit residues: 124.0987
Evaluate side-chains
  70 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   53 GLU
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 106 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 33 optimal weight:   30.0000
   chunk 60 optimal weight:    6.9990
   chunk 80 optimal weight:   30.0000
   chunk 83 optimal weight:    0.2980
   chunk 11 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    5.6588

-------------------------------------------------------------------------------
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 = 0.2976 r_free = 0.2976 target = 0.068673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.055592 restraints weight = 20484.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.2719 rms_B_bonded: 3.10
r_work: 0.2563 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8842
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10332  Z= 0.169
  Angle     :  0.573   9.193  14016  Z= 0.316
  Chirality :  0.043   0.136   1368
  Planarity :  0.004   0.058   1854
  Dihedral  :  5.153  26.024   1377
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.91 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.96 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.55 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.68 (0.21), residues: 588
  loop : -1.25 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 420 
 HIS   0.003   0.001   HIS C 113 
 PHE   0.005   0.001   PHE B  58 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02750 (  560)
  hydrogen bonds       : angle       5.16291 ( 1551)
  SS BOND              : bond        0.00522 (    3)
  SS BOND              : angle       3.68000 (    6)
  covalent geometry    : bond        0.00379 (10329)
  covalent geometry    : angle       0.56763 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: A  130 GLU cc_start: 0.8984 (tt0) cc_final: 0.8752 (pt0)
REVERT: A  195 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8082 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9013 (tt0) cc_final: 0.8637 (tm-30)
REVERT: B   53 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: B   75 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8088 (mt-10)
REVERT: B   93 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7381 (pm20)
REVERT: B  148 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7932 (mt-10)
REVERT: B  179 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8677 (mpp)
REVERT: B  188 GLU cc_start: 0.9071 (tt0) cc_final: 0.8818 (tt0)
REVERT: C  100 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8751 (pp)
REVERT: C  130 GLU cc_start: 0.8972 (tt0) cc_final: 0.8577 (pt0)
REVERT: C  148 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7463 (mt-10)
  outliers start: 15
  outliers final: 6
  residues processed: 79
  average time/residue: 1.4938
  time to fit residues: 126.0646
Evaluate side-chains
  73 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  166 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 112 optimal weight:   20.0000
   chunk 119 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 118 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   chunk 82 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 123 optimal weight:    7.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.070074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.057031 restraints weight = 20215.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 3.11
r_work: 0.2593 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10332  Z= 0.122
  Angle     :  0.549   7.157  14016  Z= 0.305
  Chirality :  0.043   0.137   1368
  Planarity :  0.004   0.057   1854
  Dihedral  :  5.033  25.775   1377
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.83 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.45 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.49 (0.22), residues: 1257
  helix: -5.03 (0.11), residues: 18
  sheet:  0.68 (0.20), residues: 591
  loop : -1.18 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 420 
 HIS   0.001   0.000   HIS A 275 
 PHE   0.006   0.001   PHE A  23 
 TYR   0.012   0.001   TYR C 343 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02535 (  560)
  hydrogen bonds       : angle       5.08705 ( 1551)
  SS BOND              : bond        0.00394 (    3)
  SS BOND              : angle       3.46677 (    6)
  covalent geometry    : bond        0.00270 (10329)
  covalent geometry    : angle       0.54474 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A   39 GLU cc_start: 0.8836 (pm20) cc_final: 0.8462 (pm20)
REVERT: A   53 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: A  148 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7747 (mt-10)
REVERT: A  195 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8023 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9026 (tt0) cc_final: 0.8677 (tm-30)
REVERT: B   53 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: B   75 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8127 (mt-10)
REVERT: B   93 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7419 (pm20)
REVERT: B  148 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7862 (mt-10)
REVERT: B  188 GLU cc_start: 0.9025 (tt0) cc_final: 0.8765 (tt0)
REVERT: C  100 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8734 (pp)
REVERT: C  130 GLU cc_start: 0.8935 (tt0) cc_final: 0.8480 (pt0)
REVERT: C  148 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7559 (mt-10)
REVERT: C  203 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8418 (ttm110)
  outliers start: 11
  outliers final: 3
  residues processed: 81
  average time/residue: 1.3819
  time to fit residues: 120.0215
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 35 optimal weight:   20.0000
   chunk 69 optimal weight:   20.0000
   chunk 118 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 15 optimal weight:   30.0000
   chunk 96 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    7.9992

-------------------------------------------------------------------------------
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 = 0.2911 r_free = 0.2911 target = 0.065882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.053239 restraints weight = 21024.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 3.11
r_work: 0.2514 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8819
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10332  Z= 0.226
  Angle     :  0.595   8.410  14016  Z= 0.328
  Chirality :  0.043   0.134   1368
  Planarity :  0.004   0.060   1854
  Dihedral  :  5.155  31.078   1377
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.15 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.94 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 (0.22), residues: 1257
  helix: -5.04 (0.11), residues: 18
  sheet:  0.64 (0.21), residues: 582
  loop : -1.21 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 421 
 HIS   0.003   0.001   HIS C 113 
 PHE   0.008   0.001   PHE A  23 
 TYR   0.015   0.001   TYR A 343 
 ARG   0.004   0.001   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02933 (  560)
  hydrogen bonds       : angle       5.19725 ( 1551)
  SS BOND              : bond        0.00742 (    3)
  SS BOND              : angle       3.81256 (    6)
  covalent geometry    : bond        0.00507 (10329)
  covalent geometry    : angle       0.59037 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8116 (tm-30)
REVERT: A   78 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8941 (m-30)
REVERT: A  148 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7812 (mt-10)
REVERT: A  195 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7986 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9046 (tt0) cc_final: 0.8672 (tm-30)
REVERT: B   53 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: B   75 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: B   93 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7417 (pm20)
REVERT: B  148 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: B  179 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8686 (mtm)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8810 (tt0)
REVERT: C  100 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8730 (pp)
REVERT: C  130 GLU cc_start: 0.8967 (tt0) cc_final: 0.8553 (pt0)
REVERT: C  148 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7512 (mt-10)
  outliers start: 9
  outliers final: 2
  residues processed: 69
  average time/residue: 1.4502
  time to fit residues: 107.2954
Evaluate side-chains
  69 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASP
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 93 optimal weight:    0.2980
   chunk 120 optimal weight:   10.0000
   chunk 81 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0980
   chunk 24 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    3.2786

-------------------------------------------------------------------------------
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 = 0.2994 r_free = 0.2994 target = 0.069721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.056650 restraints weight = 20271.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.2735 rms_B_bonded: 3.12
r_work: 0.2575 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10332  Z= 0.121
  Angle     :  0.557   8.542  14016  Z= 0.306
  Chirality :  0.043   0.130   1368
  Planarity :  0.004   0.057   1854
  Dihedral  :  4.983  27.292   1377
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.91 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.35 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.48 (0.22), residues: 1257
  helix: -5.02 (0.11), residues: 18
  sheet:  0.67 (0.20), residues: 591
  loop : -1.15 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 420 
 HIS   0.001   0.000   HIS A 275 
 PHE   0.009   0.001   PHE A  23 
 TYR   0.012   0.001   TYR B 343 
 ARG   0.003   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02484 (  560)
  hydrogen bonds       : angle       5.05146 ( 1551)
  SS BOND              : bond        0.00579 (    3)
  SS BOND              : angle       2.95845 (    6)
  covalent geometry    : bond        0.00269 (10329)
  covalent geometry    : angle       0.55325 (14010)

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

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

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2514 Ramachandran restraints generated.
    1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A   39 GLU cc_start: 0.8813 (pm20) cc_final: 0.8470 (pm20)
REVERT: A   53 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: A  195 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9050 (tt0) cc_final: 0.8680 (tm-30)
REVERT: B   53 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: B   75 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8107 (mt-10)
REVERT: B   93 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7365 (pm20)
REVERT: B  148 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7835 (mt-10)
REVERT: B  179 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8661 (mpp)
REVERT: B  188 GLU cc_start: 0.9031 (tt0) cc_final: 0.8766 (tt0)
REVERT: C  100 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8736 (pp)
REVERT: C  130 GLU cc_start: 0.8935 (tt0) cc_final: 0.8671 (pt0)
REVERT: C  148 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7468 (mt-10)
  outliers start: 11
  outliers final: 2
  residues processed: 77
  average time/residue: 1.5450
  time to fit residues: 126.7108
Evaluate side-chains
  69 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ARG
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue  100 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 100 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 92 optimal weight:   20.0000
   chunk 85 optimal weight:   30.0000
   chunk 32 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 102 optimal weight:    1.9990
   chunk 72 optimal weight:   30.0000
   chunk 114 optimal weight:    6.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.2977 r_free = 0.2977 target = 0.068853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.055873 restraints weight = 20304.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 3.09
r_work: 0.2565 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10332  Z= 0.165
  Angle     :  0.568   8.394  14016  Z= 0.312
  Chirality :  0.043   0.195   1368
  Planarity :  0.004   0.060   1854
  Dihedral  :  5.014  27.258   1377
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.75 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 12.84 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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: -0.54 (0.22), residues: 1257
  helix: -5.03 (0.11), residues: 18
  sheet:  0.59 (0.20), residues: 603
  loop : -1.18 (0.22), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  51 
 HIS   0.002   0.001   HIS C 113 
 PHE   0.006   0.001   PHE A  23 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.004   0.000   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02639 (  560)
  hydrogen bonds       : angle       5.06912 ( 1551)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       4.30968 (    6)
  covalent geometry    : bond        0.00370 (10329)
  covalent geometry    : angle       0.56114 (14010)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4494.60 seconds
wall clock time: 78 minutes 52.77 seconds (4732.77 seconds total)