Starting phenix.real_space_refine
on Sat Aug 23 04:11:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7v_15903/08_2025/8b7v_15903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7v_15903/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7v_15903/08_2025/8b7v_15903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7v_15903/08_2025/8b7v_15903.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7v_15903/08_2025/8b7v_15903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7v_15903/08_2025/8b7v_15903.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.05, per 1000 atoms: 0.20
  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: 0.65
  Conformation dependent library (CDL) restraints added in 274.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.25
  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: 1.19

  Time building geometry restraints manager: 0.87 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: 0.01
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:             0.110
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.330
  Find NCS groups from input model:        0.090
  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:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.880
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (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
 ARG   0.042   0.005   ARG B  33 
 TYR   0.211   0.022   TYR C 118 
 PHE   0.076   0.011   PHE C 254 
 TRP   0.100   0.015   TRP A  51 
 HIS   0.012   0.003   HIS A   4 

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

*********************** 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  : 0.325 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 2
  residues processed: 146
  average time/residue: 0.6151
  time to fit residues: 95.2746
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  : 0.346 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.4980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 123 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    3.4786

-------------------------------------------------------------------------------
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  70 GLN
B  90 ASN
C  70 GLN
C 159 ASN
C 165 ASN
C 341 ASN
C 386 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.073293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.060392 restraints weight = 20118.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.2806 rms_B_bonded: 3.04
r_work: 0.2652 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10332  Z= 0.150
  Angle     :  0.626   5.540  14016  Z= 0.359
  Chirality :  0.045   0.152   1368
  Planarity :  0.004   0.061   1854
  Dihedral  :  6.290  61.789   1381
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.43 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  9.02 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.21), residues: 1257
  helix: -4.95 (0.14), residues: 18
  sheet:  1.42 (0.19), residues: 582
  loop : -1.52 (0.20), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 360 
 TYR   0.012   0.001   TYR A 343 
 PHE   0.011   0.001   PHE B  23 
 TRP   0.015   0.001   TRP B 120 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10329)
  covalent geometry    : angle       0.62174 (14010)
  SS BOND              : bond        0.00856 (    3)
  SS BOND              : angle       3.41051 (    6)
  hydrogen bonds       : bond        0.03512 (  560)
  hydrogen bonds       : angle       5.71318 ( 1551)

*********************** 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
  101 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7717 (mt-10)
REVERT: A   53 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8100 (tm-30)
REVERT: B   49 GLU cc_start: 0.8960 (tt0) cc_final: 0.8676 (tm-30)
REVERT: B   53 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: B  148 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7789 (mt-10)
REVERT: B  188 GLU cc_start: 0.9045 (tt0) cc_final: 0.8840 (tt0)
  outliers start: 23
  outliers final: 0
  residues processed: 90
  average time/residue: 0.5469
  time to fit residues: 52.7515
Evaluate side-chains
  58 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 123 optimal weight:    0.0370
   chunk 1 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 116 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 78 optimal weight:    9.9990
   chunk 104 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    5.1664

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

Flipped N/Q/H residues before XYZ refinement:
C   4 HIS
C 416 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.070279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.057188 restraints weight = 20255.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 3.11
r_work: 0.2605 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10332  Z= 0.163
  Angle     :  0.582   8.404  14016  Z= 0.327
  Chirality :  0.044   0.156   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.530  23.704   1377
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.67 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.21), residues: 1257
  helix: -5.01 (0.12), residues: 18
  sheet:  1.11 (0.19), residues: 594
  loop : -1.42 (0.20), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 360 
 TYR   0.015   0.001   TYR A 343 
 PHE   0.008   0.001   PHE B  23 
 TRP   0.012   0.001   TRP A  51 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (10329)
  covalent geometry    : angle       0.58005 (14010)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       2.35646 (    6)
  hydrogen bonds       : bond        0.03134 (  560)
  hydrogen bonds       : angle       5.41018 ( 1551)

*********************** 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
  90 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: B   39 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8502 (pm20)
REVERT: B   49 GLU cc_start: 0.8996 (tt0) cc_final: 0.8678 (tm-30)
REVERT: B   53 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: B   75 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8156 (mt-10)
REVERT: B  179 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8489 (mpt)
REVERT: B  188 GLU cc_start: 0.9046 (tt0) cc_final: 0.8783 (tt0)
  outliers start: 15
  outliers final: 0
  residues processed: 83
  average time/residue: 0.5853
  time to fit residues: 51.9218
Evaluate side-chains
  63 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 106 optimal weight:    0.9980
   chunk 62 optimal weight:    7.9990
   chunk 20 optimal weight:   20.0000
   chunk 80 optimal weight:   30.0000
   chunk 12 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   overall best weight:    6.1990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.069021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.055964 restraints weight = 20366.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 3.10
r_work: 0.2574 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.3139

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= 0.183
  Angle     :  0.573   8.786  14016  Z= 0.319
  Chirality :  0.044   0.157   1368
  Planarity :  0.004   0.061   1854
  Dihedral  :  5.300  20.143   1377
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.75 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.18 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.22), residues: 1257
  helix: -5.04 (0.11), residues: 18
  sheet:  1.01 (0.20), residues: 597
  loop : -1.38 (0.21), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 360 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.007   0.001   PHE A  58 
 TRP   0.011   0.001   TRP A 420 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10329)
  covalent geometry    : angle       0.57130 (14010)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       2.21116 (    6)
  hydrogen bonds       : bond        0.03016 (  560)
  hydrogen bonds       : angle       5.30327 ( 1551)

*********************** 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
  79 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: A  130 GLU cc_start: 0.9012 (tt0) cc_final: 0.8771 (pt0)
REVERT: A  417 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8627 (ppp)
REVERT: B   39 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8625 (pm20)
REVERT: B   49 GLU cc_start: 0.9000 (tt0) cc_final: 0.8669 (tm-30)
REVERT: B   53 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7938 (tm-30)
REVERT: B   75 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8138 (mt-10)
REVERT: B  179 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8501 (mpt)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8830 (tt0)
REVERT: C  130 GLU cc_start: 0.8997 (tt0) cc_final: 0.8565 (pt0)
  outliers start: 12
  outliers final: 0
  residues processed: 76
  average time/residue: 0.6077
  time to fit residues: 49.1270
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  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 121 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 15 optimal weight:   40.0000
   chunk 20 optimal weight:    7.9990
   chunk 100 optimal weight:   20.0000
   chunk 57 optimal weight:   40.0000
   chunk 3 optimal weight:    7.9990
   chunk 49 optimal weight:   20.0000
   chunk 118 optimal weight:    8.9990
   overall best weight:    7.9990

-------------------------------------------------------------------------------
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 = 0.2965 r_free = 0.2965 target = 0.067855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.054846 restraints weight = 20504.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.2706 rms_B_bonded: 3.09
r_work: 0.2550 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.3264

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= 0.226
  Angle     :  0.591   8.435  14016  Z= 0.329
  Chirality :  0.044   0.157   1368
  Planarity :  0.004   0.060   1854
  Dihedral  :  5.345  24.814   1377
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.83 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.78 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.75 (0.20), residues: 588
  loop : -1.29 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 360 
 TYR   0.015   0.001   TYR A 343 
 PHE   0.007   0.001   PHE C 398 
 TRP   0.011   0.001   TRP A 420 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (10329)
  covalent geometry    : angle       0.58399 (14010)
  SS BOND              : bond        0.00561 (    3)
  SS BOND              : angle       4.46870 (    6)
  hydrogen bonds       : bond        0.03046 (  560)
  hydrogen bonds       : angle       5.31318 ( 1551)

*********************** 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
  86 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: A  130 GLU cc_start: 0.9015 (tt0) cc_final: 0.8784 (pt0)
REVERT: B   39 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8454 (pm20)
REVERT: B   49 GLU cc_start: 0.9013 (tt0) cc_final: 0.8672 (tm-30)
REVERT: B   53 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8009 (tm-30)
REVERT: B   75 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8148 (mt-10)
REVERT: B  148 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  179 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8488 (mpt)
REVERT: B  188 GLU cc_start: 0.9076 (tt0) cc_final: 0.8778 (tt0)
REVERT: C   37 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8270 (mt-10)
REVERT: C  130 GLU cc_start: 0.8998 (tt0) cc_final: 0.8583 (pt0)
REVERT: C  148 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7636 (mt-10)
  outliers start: 17
  outliers final: 5
  residues processed: 79
  average time/residue: 0.6107
  time to fit residues: 51.5545
Evaluate side-chains
  68 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 CYS
Chi-restraints excluded: chain A residue  280 MET
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  417 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 63 optimal weight:   20.0000
   chunk 114 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 83 optimal weight:   30.0000
   chunk 94 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 48 optimal weight:    8.9990
   chunk 125 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.2968 r_free = 0.2968 target = 0.068043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.055016 restraints weight = 20555.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.2712 rms_B_bonded: 3.12
r_work: 0.2553 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10332  Z= 0.205
  Angle     :  0.575   6.995  14016  Z= 0.321
  Chirality :  0.043   0.157   1368
  Planarity :  0.004   0.059   1854
  Dihedral  :  5.265  23.504   1377
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.67 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.67 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.80 (0.20), residues: 600
  loop : -1.37 (0.21), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 360 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.006   0.001   PHE B  58 
 TRP   0.011   0.001   TRP C  51 
 HIS   0.003   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (10329)
  covalent geometry    : angle       0.56944 (14010)
  SS BOND              : bond        0.00350 (    3)
  SS BOND              : angle       4.04681 (    6)
  hydrogen bonds       : bond        0.02956 (  560)
  hydrogen bonds       : angle       5.27899 ( 1551)

*********************** 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
  83 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: A   78 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (m-30)
REVERT: A  130 GLU cc_start: 0.9007 (tt0) cc_final: 0.8785 (pt0)
REVERT: A  195 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8056 (ptm-80)
REVERT: B   39 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8572 (pm20)
REVERT: B   49 GLU cc_start: 0.8999 (tt0) cc_final: 0.8673 (tm-30)
REVERT: B   53 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7959 (tm-30)
REVERT: B   75 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8172 (mt-10)
REVERT: B  148 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: B  179 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8485 (mpt)
REVERT: B  188 GLU cc_start: 0.9074 (tt0) cc_final: 0.8832 (tt0)
REVERT: C  100 ILE cc_start: 0.9104 (tp) cc_final: 0.8754 (pp)
REVERT: C  130 GLU cc_start: 0.9000 (tt0) cc_final: 0.8608 (pt0)
REVERT: C  148 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7559 (mt-10)
  outliers start: 16
  outliers final: 4
  residues processed: 78
  average time/residue: 0.6380
  time to fit residues: 52.7838
Evaluate side-chains
  67 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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 B residue   39 GLU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   chunk 122 optimal weight:   20.0000
   chunk 71 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.2970 r_free = 0.2970 target = 0.068246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.055223 restraints weight = 20437.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 3.09
r_work: 0.2555 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.3431

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= 0.186
  Angle     :  0.568   7.480  14016  Z= 0.316
  Chirality :  0.043   0.157   1368
  Planarity :  0.004   0.058   1854
  Dihedral  :  5.205  24.906   1377
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.83 %
    Favored  : 98.01 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.67 (0.20), residues: 588
  loop : -1.27 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 360 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.006   0.001   PHE B  58 
 TRP   0.010   0.001   TRP A 420 
 HIS   0.002   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10329)
  covalent geometry    : angle       0.56342 (14010)
  SS BOND              : bond        0.00456 (    3)
  SS BOND              : angle       3.59516 (    6)
  hydrogen bonds       : bond        0.02845 (  560)
  hydrogen bonds       : angle       5.23211 ( 1551)

*********************** 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
  73 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8071 (tm-30)
REVERT: A   78 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8967 (m-30)
REVERT: A  130 GLU cc_start: 0.8975 (tt0) cc_final: 0.8761 (pt0)
REVERT: A  195 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8039 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9012 (tt0) cc_final: 0.8673 (tm-30)
REVERT: B   53 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: B   75 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8150 (mt-10)
REVERT: B   93 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7378 (pm20)
REVERT: B  148 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7949 (mt-10)
REVERT: B  179 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8464 (mpt)
REVERT: B  188 GLU cc_start: 0.9071 (tt0) cc_final: 0.8824 (tt0)
REVERT: C  100 ILE cc_start: 0.9109 (tp) cc_final: 0.8777 (pp)
REVERT: C  130 GLU cc_start: 0.8979 (tt0) cc_final: 0.8571 (pt0)
REVERT: C  148 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7576 (mt-10)
  outliers start: 11
  outliers final: 3
  residues processed: 71
  average time/residue: 0.6472
  time to fit residues: 48.9738
Evaluate side-chains
  66 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
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 B residue   83 GLU
Chi-restraints excluded: chain B residue   93 GLU
Chi-restraints excluded: chain B residue  179 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 115 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 43 optimal weight:   30.0000
   chunk 23 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 105 optimal weight:   20.0000
   overall best weight:    6.7994

-------------------------------------------------------------------------------
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 = 0.2964 r_free = 0.2964 target = 0.067998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.055050 restraints weight = 20287.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 3.07
r_work: 0.2553 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.3478

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= 0.196
  Angle     :  0.578   7.890  14016  Z= 0.319
  Chirality :  0.043   0.155   1368
  Planarity :  0.004   0.057   1854
  Dihedral  :  5.166  24.581   1377
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.07 %
    Favored  : 97.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.67 (0.20), residues: 588
  loop : -1.25 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 360 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.006   0.001   PHE B  58 
 TRP   0.010   0.001   TRP C  51 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (10329)
  covalent geometry    : angle       0.57342 (14010)
  SS BOND              : bond        0.00437 (    3)
  SS BOND              : angle       3.39813 (    6)
  hydrogen bonds       : bond        0.02863 (  560)
  hydrogen bonds       : angle       5.21577 ( 1551)

*********************** 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
  77 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: A   78 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (m-30)
REVERT: A  130 GLU cc_start: 0.8980 (tt0) cc_final: 0.8772 (pt0)
REVERT: A  148 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7800 (mt-10)
REVERT: A  195 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8049 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9017 (tt0) cc_final: 0.8685 (tm-30)
REVERT: B   53 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: B   75 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: B   93 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7346 (pm20)
REVERT: B  148 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7871 (mt-10)
REVERT: B  179 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8490 (mpt)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8821 (tt0)
REVERT: C  100 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8775 (pp)
REVERT: C  130 GLU cc_start: 0.8986 (tt0) cc_final: 0.8575 (pt0)
REVERT: C  148 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7561 (mt-10)
  outliers start: 15
  outliers final: 4
  residues processed: 72
  average time/residue: 0.6300
  time to fit residues: 48.3295
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  : 0.326 
-------------------------------------------------------------------------------
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 B residue   83 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 82 optimal weight:   30.0000
   chunk 4 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 111 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.2969 r_free = 0.2969 target = 0.068394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.055390 restraints weight = 20379.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 3.11
r_work: 0.2560 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10332  Z= 0.173
  Angle     :  0.570   6.912  14016  Z= 0.315
  Chirality :  0.043   0.155   1368
  Planarity :  0.004   0.058   1854
  Dihedral  :  5.116  26.181   1377
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.83 %
    Favored  : 98.01 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.69 (0.20), residues: 588
  loop : -1.21 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 360 
 TYR   0.013   0.001   TYR A 343 
 PHE   0.005   0.001   PHE B  23 
 TRP   0.011   0.001   TRP C  51 
 HIS   0.002   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10329)
  covalent geometry    : angle       0.56545 (14010)
  SS BOND              : bond        0.00401 (    3)
  SS BOND              : angle       3.35925 (    6)
  hydrogen bonds       : bond        0.02745 (  560)
  hydrogen bonds       : angle       5.16991 ( 1551)

*********************** 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
  76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: A   78 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (m-30)
REVERT: A  130 GLU cc_start: 0.8952 (tt0) cc_final: 0.8744 (pt0)
REVERT: A  148 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7707 (mt-10)
REVERT: A  195 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8017 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9024 (tt0) cc_final: 0.8689 (tm-30)
REVERT: B   53 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: B   75 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: B   93 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7354 (pm20)
REVERT: B  148 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: B  179 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8486 (mpt)
REVERT: B  188 GLU cc_start: 0.9067 (tt0) cc_final: 0.8814 (tt0)
REVERT: C  100 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8753 (pp)
REVERT: C  130 GLU cc_start: 0.8971 (tt0) cc_final: 0.8570 (pt0)
REVERT: C  148 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7525 (mt-10)
  outliers start: 11
  outliers final: 6
  residues processed: 73
  average time/residue: 0.6478
  time to fit residues: 50.2038
Evaluate side-chains
  72 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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  308 VAL
Chi-restraints excluded: chain B residue   83 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 57 optimal weight:   40.0000
   chunk 112 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 88 optimal weight:    8.9990
   chunk 114 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 118 optimal weight:    8.9990
   chunk 116 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 45 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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 = 0.2962 r_free = 0.2962 target = 0.068008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.055078 restraints weight = 20305.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 3.07
r_work: 0.2550 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8849
moved from start:          0.3549

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= 0.205
  Angle     :  0.590  10.384  14016  Z= 0.323
  Chirality :  0.043   0.156   1368
  Planarity :  0.004   0.062   1854
  Dihedral  :  5.127  26.178   1377
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.15 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.22), residues: 1257
  helix: -5.05 (0.11), residues: 18
  sheet:  0.66 (0.20), residues: 588
  loop : -1.20 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 360 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.009   0.001   PHE C 117 
 TRP   0.016   0.001   TRP A  94 
 HIS   0.002   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (10329)
  covalent geometry    : angle       0.58605 (14010)
  SS BOND              : bond        0.00416 (    3)
  SS BOND              : angle       3.39263 (    6)
  hydrogen bonds       : bond        0.02833 (  560)
  hydrogen bonds       : angle       5.18796 ( 1551)

********************** 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
  71 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A  130 GLU cc_start: 0.8989 (tt0) cc_final: 0.8770 (pt0)
REVERT: A  148 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: A  195 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8045 (ptm-80)
REVERT: B   49 GLU cc_start: 0.9032 (tt0) cc_final: 0.8699 (tm-30)
REVERT: B   53 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: B   75 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8095 (mt-10)
REVERT: B   93 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7348 (pm20)
REVERT: B  148 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: B  179 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8479 (mpt)
REVERT: B  188 GLU cc_start: 0.9069 (tt0) cc_final: 0.8819 (tt0)
REVERT: C  100 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8761 (pp)
REVERT: C  130 GLU cc_start: 0.8981 (tt0) cc_final: 0.8582 (pt0)
REVERT: C  148 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7483 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 0.6576
  time to fit residues: 47.5366
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  : 0.246 
-------------------------------------------------------------------------------
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 A residue  308 VAL
Chi-restraints excluded: chain B residue   83 GLU
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 63 optimal weight:   20.0000
   chunk 72 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 106 optimal weight:   20.0000
   chunk 69 optimal weight:    8.9990
   chunk 124 optimal weight:   30.0000
   chunk 99 optimal weight:   40.0000
   chunk 116 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 76 optimal weight:   20.0000
   chunk 8 optimal weight:    6.9990
   overall best weight:    7.3992

-------------------------------------------------------------------------------
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 = 0.2905 r_free = 0.2905 target = 0.065675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.053221 restraints weight = 20826.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 3.08
r_work: 0.2515 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.3549

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= 0.210
  Angle     :  0.593  10.181  14016  Z= 0.325
  Chirality :  0.043   0.157   1368
  Planarity :  0.004   0.064   1854
  Dihedral  :  5.160  26.308   1377
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.23 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 12.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.22), residues: 1257
  helix: -5.06 (0.11), residues: 18
  sheet:  0.64 (0.20), residues: 588
  loop : -1.20 (0.21), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  33 
 TYR   0.014   0.001   TYR A 343 
 PHE   0.007   0.001   PHE C 117 
 TRP   0.017   0.001   TRP A  94 
 HIS   0.003   0.001   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (10329)
  covalent geometry    : angle       0.58909 (14010)
  SS BOND              : bond        0.00440 (    3)
  SS BOND              : angle       3.39210 (    6)
  hydrogen bonds       : bond        0.02880 (  560)
  hydrogen bonds       : angle       5.21186 ( 1551)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1788.89 seconds
wall clock time: 31 minutes 35.26 seconds (1895.26 seconds total)