Starting phenix.real_space_refine
on Sat May  2 09:37:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpe_22286/05_2026/6xpe_22286.cif"
  }
  resolution = 4.1
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      8      6.06       5
     S      32      5.16       5
     C    2806      2.51       5
     N     692      2.21       5
     O     754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4292
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' ZN': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2158  SG  CYS A  53      34.917  42.485  22.387  1.00140.11           S
  ATOM   2079  SG  CYS B 361      36.563  50.333  26.866  1.00135.63           S
  ATOM   2104  SG  CYS B 364      39.360  48.066  24.716  1.00130.17           S
  ATOM     16  SG  CYS B  53      39.783  23.915  22.387  1.00140.11           S
  ATOM   4221  SG  CYS A 361      38.137  16.067  26.866  1.00135.63           S
  ATOM   4246  SG  CYS A 364      35.340  18.334  24.716  1.00130.17           S

  Time building chain proxies: 1.14, per 1000 atoms: 0.27
  Number of scatterers: 4292
  At special positions: 0
  Unit cell: (75.53, 67.23, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      8     29.99
     S      32     16.00
     O     754      8.00
     N     692      7.00
     C    2806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.29
  Conformation dependent library (CDL) restraints added in 226.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  52 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 361 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 364 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  54 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS A 301 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 318 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS B  53 "
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  52 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 361 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  54 "
      pdb="  ZN A 404 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 137 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 345 "
      pdb="  ZN A 405 "
        pdb="ZN    ZN A 405 " - pdb=" NE2 HIS A 106 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 318 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 301 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  53 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 137 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 345 "
      pdb="  ZN B 403 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B 106 "
      Number of angles added : 4


  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      62.5% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B  76 " --> pdb=" O   TRP B  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 124
      removed outlier: 4.324A  pdb=" N   LEU B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 181 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL B 219 " --> pdb=" O   ARG B 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL B 231 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 257 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR B 265 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP B 269 " --> pdb=" O   THR B 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE B 272 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 274 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG B 331 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS B 336 " --> pdb=" O   ARG B 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 124
      removed outlier: 3.821A  pdb=" N   LEU A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU A 116 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS A 336 " --> pdb=" O   ARG A 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS B 318 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS A 318 " --> pdb=" O   SER A 302 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    708 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: 0.68

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1298
        1.34 -     1.46: 834
        1.46 -     1.57: 2192
        1.57 -     1.69: 2
        1.69 -     1.81: 44
  Bond restraints: 4370
  Sorted by residual:
  bond pdb=" N   HIS B 106 "
       pdb=" CA  HIS B 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.397  0.062 1.20e-02 6.94e+03 2.68e+01
  bond pdb=" CA  PRO B 354 "
       pdb=" C   PRO B 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  PRO A 354 "
       pdb=" C   PRO A 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  VAL A 355 "
       pdb=" C   VAL A 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  bond pdb=" CA  VAL B 355 "
       pdb=" C   VAL B 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  ... (remaining 4365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 5750
        1.93 -     3.87: 148
        3.87 -     5.80: 32
        5.80 -     7.74: 7
        7.74 -     9.67: 3
  Bond angle restraints: 5940
  Sorted by residual:
  angle pdb=" C   VAL A 355 "
        pdb=" N   ASP A 356 "
        pdb=" CA  ASP A 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   VAL B 355 "
        pdb=" N   ASP B 356 "
        pdb=" CA  ASP B 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   PHE A 114 "
        pdb=" N   LEU A 115 "
        pdb=" CA  LEU A 115 "
      ideal   model   delta    sigma   weight residual
     120.82  127.96   -7.14 1.50e+00 4.44e-01 2.26e+01
  angle pdb=" N   PHE A 114 "
        pdb=" CA  PHE A 114 "
        pdb=" C   PHE A 114 "
      ideal   model   delta    sigma   weight residual
     110.80  120.47   -9.67 2.13e+00 2.20e-01 2.06e+01
  angle pdb=" N   VAL B 355 "
        pdb=" CA  VAL B 355 "
        pdb=" C   VAL B 355 "
      ideal   model   delta    sigma   weight residual
     109.34  116.94   -7.60 2.08e+00 2.31e-01 1.33e+01
  ... (remaining 5935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.89: 2155
       11.89 -    23.79: 264
       23.79 -    35.68: 120
       35.68 -    47.57: 41
       47.57 -    59.47: 10
  Dihedral angle restraints: 2590
    sinusoidal: 952
      harmonic: 1638
  Sorted by residual:
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   THR B 309 "
           pdb=" CA  THR B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   THR A 309 "
           pdb=" CA  THR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  PRO A 354 "
           pdb=" C   PRO A 354 "
           pdb=" N   VAL A 355 "
           pdb=" CA  VAL A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.06   23.94     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 666
       0.067 -    0.135: 73
       0.135 -    0.202: 2
       0.202 -    0.269: 0
       0.269 -    0.337: 1
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CA  PHE A 114 "
            pdb=" N   PHE A 114 "
            pdb=" C   PHE A 114 "
            pdb=" CB  PHE A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  ILE B 305 "
            pdb=" CA  ILE B 305 "
            pdb=" CG1 ILE B 305 "
            pdb=" CG2 ILE B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 739 not shown)

  Planarity restraints: 706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 105 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   ALA B 105 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA B 105 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   HIS B 106 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 106 "   -0.019 2.00e-02 2.50e+03   2.17e-02 7.08e+00
        pdb=" CG  HIS B 106 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 106 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 106 "    0.014 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 106 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 248 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 249 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 249 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 249 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 703 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 9
        2.17 -     2.86: 1745
        2.86 -     3.54: 6492
        3.54 -     4.22: 9384
        4.22 -     4.90: 15752
  Nonbonded interactions: 33382
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.492 2.230
  nonbonded pdb=" OD2 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.514 2.230
  nonbonded pdb=" OD1 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.590 2.230
  nonbonded pdb=" CG  ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.615 2.460
  nonbonded pdb=" OD1 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.619 2.230
  ... (remaining 33377 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 52 through 403)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.740
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
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      :  0.021   0.575   4390  Z= 0.670
  Angle     :  0.912  21.804   5944  Z= 0.467
  Chirality :  0.044   0.337    742
  Planarity :  0.004   0.043    706
  Dihedral  : 14.302  59.467   1510
  Min Nonbonded Distance : 1.492

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.57 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -5.36 (0.30), residues: 530
  helix: -3.29 (0.21), residues: 332
  sheet: -4.09 (0.59), residues: 44
  loop : -3.38 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 131 
 TYR   0.007   0.001   TYR B 160 
 PHE   0.012   0.001   PHE B 218 
 TRP   0.005   0.001   TRP B 122 
 HIS   0.025   0.002   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 ( 4370)
  covalent geometry    : angle       0.81930 ( 5940)
  hydrogen bonds       : bond        0.30609 (  236)
  hydrogen bonds       : angle      10.60469 (  708)
  metal coordination   : bond        0.29794 (   20)
  metal coordination   : angle      15.50205 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.9142 (tp40) cc_final: 0.8608 (tm-30)
REVERT: B  310 MET cc_start: 0.7366 (mmm) cc_final: 0.7068 (mtp)
REVERT: A  227 GLN cc_start: 0.9131 (tp40) cc_final: 0.8593 (tm-30)
REVERT: A  310 MET cc_start: 0.7360 (mmm) cc_final: 0.7074 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 75
  average time/residue: 0.0888
  time to fit residues: 8.2482
Evaluate side-chains
  52 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
B 211 ASN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.085691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.069481 restraints weight = 13426.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.071332 restraints weight = 7933.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.072590 restraints weight = 5585.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.073498 restraints weight = 4440.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.073865 restraints weight = 3818.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4390  Z= 0.148
  Angle     :  0.616   5.930   5944  Z= 0.320
  Chirality :  0.043   0.229    742
  Planarity :  0.005   0.036    706
  Dihedral  :  4.854  26.507    572
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.62 (0.36), residues: 530
  helix: -1.00 (0.27), residues: 342
  sheet: -2.72 (0.70), residues: 40
  loop : -2.89 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 331 
 TYR   0.007   0.001   TYR A 284 
 PHE   0.018   0.002   PHE A 114 
 TRP   0.013   0.002   TRP A 122 
 HIS   0.006   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4370)
  covalent geometry    : angle       0.61541 ( 5940)
  hydrogen bonds       : bond        0.05256 (  236)
  hydrogen bonds       : angle       4.70089 (  708)
  metal coordination   : bond        0.01105 (   20)
  metal coordination   : angle       1.25964 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.8904 (tp40) cc_final: 0.8643 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0447
  time to fit residues: 4.6772
Evaluate side-chains
  41 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 15 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.086220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.069886 restraints weight = 12968.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071782 restraints weight = 7696.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.072989 restraints weight = 5434.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.073850 restraints weight = 4377.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.074395 restraints weight = 3770.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.3694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4390  Z= 0.149
  Angle     :  0.607   7.112   5944  Z= 0.308
  Chirality :  0.040   0.120    742
  Planarity :  0.004   0.038    706
  Dihedral  :  4.583  23.201    572
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -1.61 (0.37), residues: 530
  helix: -0.12 (0.28), residues: 342
  sheet: -1.95 (0.69), residues: 44
  loop : -2.91 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 331 
 TYR   0.019   0.002   TYR B  69 
 PHE   0.021   0.002   PHE B 114 
 TRP   0.009   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4370)
  covalent geometry    : angle       0.60631 ( 5940)
  hydrogen bonds       : bond        0.04375 (  236)
  hydrogen bonds       : angle       4.07405 (  708)
  metal coordination   : bond        0.00239 (   20)
  metal coordination   : angle       1.45929 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.8768 (tp40) cc_final: 0.8522 (tm-30)
REVERT: B  365 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: A  109 ILE cc_start: 0.8968 (mt) cc_final: 0.8623 (tp)
REVERT: A  365 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7680 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0637
  time to fit residues: 5.9823
Evaluate side-chains
  45 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.086458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.070238 restraints weight = 12469.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.071963 restraints weight = 7654.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.073159 restraints weight = 5524.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.073995 restraints weight = 4458.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.074604 restraints weight = 3862.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4390  Z= 0.155
  Angle     :  0.612   6.920   5944  Z= 0.310
  Chirality :  0.040   0.125    742
  Planarity :  0.005   0.043    706
  Dihedral  :  4.509  24.085    572
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -1.19 (0.37), residues: 530
  helix:  0.25 (0.29), residues: 342
  sheet: -2.05 (0.68), residues: 48
  loop : -2.80 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 331 
 TYR   0.010   0.001   TYR B 284 
 PHE   0.012   0.002   PHE B 119 
 TRP   0.007   0.001   TRP B 122 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4370)
  covalent geometry    : angle       0.61095 ( 5940)
  hydrogen bonds       : bond        0.03968 (  236)
  hydrogen bonds       : angle       3.77642 (  708)
  metal coordination   : bond        0.00269 (   20)
  metal coordination   : angle       1.44855 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 LEU cc_start: 0.8936 (tp) cc_final: 0.8695 (tp)
REVERT: B  340 LYS cc_start: 0.9361 (ptmt) cc_final: 0.9106 (pttm)
REVERT: A  109 ILE cc_start: 0.8991 (mt) cc_final: 0.8648 (tp)
REVERT: A  340 LYS cc_start: 0.9369 (ptmt) cc_final: 0.9112 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0743
  time to fit residues: 7.2036
Evaluate side-chains
  46 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 23 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.088338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.071900 restraints weight = 13089.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.073610 restraints weight = 7888.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.075013 restraints weight = 5700.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075789 restraints weight = 4516.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.076404 restraints weight = 3903.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4390  Z= 0.156
  Angle     :  0.602   7.670   5944  Z= 0.309
  Chirality :  0.040   0.122    742
  Planarity :  0.004   0.038    706
  Dihedral  :  4.546  23.425    572
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -1.18 (0.37), residues: 530
  helix:  0.28 (0.29), residues: 342
  sheet: -1.82 (0.70), residues: 46
  loop : -2.94 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 331 
 TYR   0.014   0.001   TYR B  69 
 PHE   0.022   0.002   PHE B 342 
 TRP   0.030   0.002   TRP B 152 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4370)
  covalent geometry    : angle       0.60172 ( 5940)
  hydrogen bonds       : bond        0.04075 (  236)
  hydrogen bonds       : angle       3.87014 (  708)
  metal coordination   : bond        0.00219 (   20)
  metal coordination   : angle       1.26775 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ILE cc_start: 0.8992 (mt) cc_final: 0.8676 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0542
  time to fit residues: 5.3403
Evaluate side-chains
  50 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 18 optimal weight:    0.0470
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 53 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.6884

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

Flipped N/Q/H residues before XYZ refinement:
B 328 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.089721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.073361 restraints weight = 13154.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.075224 restraints weight = 7947.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.076548 restraints weight = 5643.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.077143 restraints weight = 4512.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.077856 restraints weight = 3984.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4390  Z= 0.121
  Angle     :  0.569   6.499   5944  Z= 0.287
  Chirality :  0.040   0.117    742
  Planarity :  0.004   0.036    706
  Dihedral  :  4.343  22.403    572
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.84 (0.38), residues: 530
  helix:  0.54 (0.30), residues: 338
  sheet: -1.44 (0.75), residues: 46
  loop : -2.83 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 331 
 TYR   0.006   0.001   TYR A 284 
 PHE   0.018   0.002   PHE B 342 
 TRP   0.010   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4370)
  covalent geometry    : angle       0.56628 ( 5940)
  hydrogen bonds       : bond        0.03563 (  236)
  hydrogen bonds       : angle       3.53779 (  708)
  metal coordination   : bond        0.00237 (   20)
  metal coordination   : angle       2.14843 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8644 (t) cc_final: 0.8170 (p)
REVERT: B  365 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A   75 CYS cc_start: 0.8622 (t) cc_final: 0.8172 (p)
REVERT: A  109 ILE cc_start: 0.9104 (mt) cc_final: 0.8834 (tp)
REVERT: A  365 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7725 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0533
  time to fit residues: 5.0913
Evaluate side-chains
  46 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 328 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.089344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.072419 restraints weight = 13138.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.074277 restraints weight = 7740.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075691 restraints weight = 5506.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.076471 restraints weight = 4356.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.077035 restraints weight = 3774.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4390  Z= 0.150
  Angle     :  0.638   8.252   5944  Z= 0.317
  Chirality :  0.040   0.122    742
  Planarity :  0.004   0.035    706
  Dihedral  :  4.339  23.480    572
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.76 (0.38), residues: 530
  helix:  0.55 (0.30), residues: 340
  sheet: -1.05 (0.77), residues: 46
  loop : -2.83 (0.48), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 331 
 TYR   0.014   0.001   TYR B  69 
 PHE   0.016   0.002   PHE B 342 
 TRP   0.006   0.001   TRP B 306 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4370)
  covalent geometry    : angle       0.63653 ( 5940)
  hydrogen bonds       : bond        0.03747 (  236)
  hydrogen bonds       : angle       3.70334 (  708)
  metal coordination   : bond        0.00230 (   20)
  metal coordination   : angle       1.87032 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8699 (t) cc_final: 0.8196 (p)
REVERT: A   75 CYS cc_start: 0.8688 (t) cc_final: 0.8162 (p)
REVERT: A  109 ILE cc_start: 0.9133 (mt) cc_final: 0.8890 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0550
  time to fit residues: 4.8337
Evaluate side-chains
  46 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 328 GLN
A 328 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.088317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.071476 restraints weight = 12864.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.073315 restraints weight = 7904.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.074609 restraints weight = 5695.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.075319 restraints weight = 4593.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.075922 restraints weight = 4018.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4390  Z= 0.172
  Angle     :  0.662   7.189   5944  Z= 0.327
  Chirality :  0.041   0.125    742
  Planarity :  0.004   0.034    706
  Dihedral  :  4.497  24.408    572
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.65 (0.38), residues: 530
  helix:  0.48 (0.30), residues: 348
  sheet: -0.80 (0.79), residues: 46
  loop : -2.57 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 331 
 TYR   0.008   0.001   TYR B 284 
 PHE   0.024   0.002   PHE A 342 
 TRP   0.006   0.001   TRP B 152 
 HIS   0.003   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4370)
  covalent geometry    : angle       0.66069 ( 5940)
  hydrogen bonds       : bond        0.03967 (  236)
  hydrogen bonds       : angle       3.69846 (  708)
  metal coordination   : bond        0.00260 (   20)
  metal coordination   : angle       1.51041 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8721 (t) cc_final: 0.8193 (p)
REVERT: A   75 CYS cc_start: 0.8694 (t) cc_final: 0.8172 (p)
REVERT: A  109 ILE cc_start: 0.9072 (mt) cc_final: 0.8839 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0569
  time to fit residues: 4.9942
Evaluate side-chains
  43 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 227 GLN
B 328 GLN
A 328 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.089615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.073097 restraints weight = 12605.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.074865 restraints weight = 7721.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076177 restraints weight = 5559.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.076885 restraints weight = 4459.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.077472 restraints weight = 3887.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4390  Z= 0.135
  Angle     :  0.622   8.090   5944  Z= 0.309
  Chirality :  0.040   0.126    742
  Planarity :  0.004   0.034    706
  Dihedral  :  4.422  23.201    572
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.25 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.39), residues: 530
  helix:  0.65 (0.30), residues: 342
  sheet: -0.60 (0.83), residues: 46
  loop : -2.53 (0.49), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 331 
 TYR   0.013   0.001   TYR B  69 
 PHE   0.023   0.002   PHE B 114 
 TRP   0.009   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4370)
  covalent geometry    : angle       0.61972 ( 5940)
  hydrogen bonds       : bond        0.03711 (  236)
  hydrogen bonds       : angle       3.72808 (  708)
  metal coordination   : bond        0.00215 (   20)
  metal coordination   : angle       2.22393 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8394 (tm-30)
REVERT: A  109 ILE cc_start: 0.9077 (mt) cc_final: 0.8871 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0561
  time to fit residues: 5.3657
Evaluate side-chains
  45 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0050
   chunk 46 optimal weight:    0.0770
   overall best weight:    0.3490

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.093838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.077319 restraints weight = 12686.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.079319 restraints weight = 7469.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.080489 restraints weight = 5199.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.081519 restraints weight = 4177.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.082075 restraints weight = 3552.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4390  Z= 0.111
  Angle     :  0.616   8.072   5944  Z= 0.298
  Chirality :  0.039   0.125    742
  Planarity :  0.004   0.036    706
  Dihedral  :  4.065  17.344    572
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.18 (0.39), residues: 530
  helix:  0.81 (0.30), residues: 342
  sheet: -0.12 (0.90), residues: 40
  loop : -2.29 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 331 
 TYR   0.004   0.001   TYR B  69 
 PHE   0.016   0.001   PHE A 342 
 TRP   0.011   0.001   TRP B 122 
 HIS   0.004   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4370)
  covalent geometry    : angle       0.60866 ( 5940)
  hydrogen bonds       : bond        0.02973 (  236)
  hydrogen bonds       : angle       3.25895 (  708)
  metal coordination   : bond        0.00444 (   20)
  metal coordination   : angle       3.63594 (    4)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8679 (t) cc_final: 0.8240 (p)
REVERT: B  146 LEU cc_start: 0.9155 (tp) cc_final: 0.8944 (tp)
REVERT: B  365 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7946 (tm-30)
REVERT: A   75 CYS cc_start: 0.8621 (t) cc_final: 0.8205 (p)
REVERT: A  146 LEU cc_start: 0.9161 (tp) cc_final: 0.8958 (tp)
REVERT: A  227 GLN cc_start: 0.8824 (tp40) cc_final: 0.8493 (tm-30)
REVERT: A  365 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7951 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0566
  time to fit residues: 6.3108
Evaluate side-chains
  51 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 51 optimal weight:    0.6980
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.090404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.073939 restraints weight = 12753.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.075747 restraints weight = 7847.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.077003 restraints weight = 5606.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.077879 restraints weight = 4488.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.078372 restraints weight = 3877.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4390  Z= 0.132
  Angle     :  0.644   7.369   5944  Z= 0.311
  Chirality :  0.041   0.168    742
  Planarity :  0.004   0.036    706
  Dihedral  :  3.974  16.003    572
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.16 (0.39), residues: 530
  helix:  0.77 (0.30), residues: 342
  sheet: -0.37 (0.90), residues: 42
  loop : -2.07 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 331 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.013   0.001   PHE B 342 
 TRP   0.009   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4370)
  covalent geometry    : angle       0.63972 ( 5940)
  hydrogen bonds       : bond        0.03304 (  236)
  hydrogen bonds       : angle       3.33515 (  708)
  metal coordination   : bond        0.00274 (   20)
  metal coordination   : angle       2.76642 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 768.27 seconds
wall clock time: 14 minutes 2.55 seconds (842.55 seconds total)