Starting phenix.real_space_refine
on Fri Aug 22 15:28:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gsz_34244/08_2025/8gsz_34244.map"
  }
  resolution = 3.65
  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=  -0.000 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 140 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: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    3118      2.51       5
     N     854      2.21       5
     O     872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 4870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2435
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 14, 'TRANS': 295}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 22
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.53, per 1000 atoms: 0.31
  Number of scatterers: 4870
  At special positions: 0
  Unit cell: (84.609, 73.899, 106.029, 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      26     16.00
     O     872      8.00
     N     854      7.00
     C    3118      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: 0.26
  Conformation dependent library (CDL) restraints added in 135.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      62.3% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 31
      removed outlier: 3.551A  pdb=" N   ALA A  21 " --> pdb=" O   GLY A  17 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.678A  pdb=" N   GLU A  38 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 65
      removed outlier: 3.593A  pdb=" N   VAL A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY A  57 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
      removed outlier: 4.025A  pdb=" N   ARG A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS A  72 " --> pdb=" O   GLU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
    Processing helix  chain 'A' and resid 80 through 90
      removed outlier: 3.844A  pdb=" N   THR A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 4.134A  pdb=" N   ARG A  95 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU A  98 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   TYR A 104 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 134
      removed outlier: 4.115A  pdb=" N   LEU A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE A 132 " --> pdb=" O   GLN A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 3.505A  pdb=" N   LEU A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 3.590A  pdb=" N   SER A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 186
      removed outlier: 3.655A  pdb=" N   ARG A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A 186 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 273
      removed outlier: 3.717A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
      removed outlier: 3.643A  pdb=" N   ALA A 288 " --> pdb=" O   ARG A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 302
      removed outlier: 3.978A  pdb=" N   GLU A 296 " --> pdb=" O   CYS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 3.719A  pdb=" N   GLN A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASN A 307 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 302 through 307'
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 4.250A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 330 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A 335 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 31
      removed outlier: 3.551A  pdb=" N   ALA B  21 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU B  23 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL B  24 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 38
      removed outlier: 3.678A  pdb=" N   GLU B  38 " --> pdb=" O   TRP B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 65
      removed outlier: 3.593A  pdb=" N   VAL B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   SER B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 72
      removed outlier: 4.025A  pdb=" N   ARG B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   HIS B  72 " --> pdb=" O   GLU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 78
    Processing helix  chain 'B' and resid 80 through 90
      removed outlier: 3.844A  pdb=" N   THR B  84 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 108
      removed outlier: 4.134A  pdb=" N   ARG B  95 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   TYR B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 134
      removed outlier: 4.115A  pdb=" N   LEU B 124 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 132 " --> pdb=" O   GLN B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 151
      removed outlier: 3.505A  pdb=" N   LEU B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 3.590A  pdb=" N   SER B 162 " --> pdb=" O   GLY B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 186
      removed outlier: 3.655A  pdb=" N   ARG B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR B 186 " --> pdb=" O   TYR B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 273
      removed outlier: 3.717A  pdb=" N   GLN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 288
      removed outlier: 3.643A  pdb=" N   ALA B 288 " --> pdb=" O   ARG B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 302
      removed outlier: 3.978A  pdb=" N   GLU B 296 " --> pdb=" O   CYS B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 3.719A  pdb=" N   GLN B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ASN B 307 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 302 through 307'
    Processing helix  chain 'B' and resid 324 through 335
      removed outlier: 4.250A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B 330 " --> pdb=" O   SER B 326 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN B 335 " --> pdb=" O   ARG B 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249
      removed outlier: 3.691A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU A 249 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ARG A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249
      removed outlier: 3.691A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   GLU B 249 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   ARG B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    612 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: 0.69

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1588
        1.34 -     1.46: 1126
        1.46 -     1.58: 2226
        1.58 -     1.70: 0
        1.70 -     1.81: 32
  Bond restraints: 4972
  Sorted by residual:
  bond pdb=" N   VAL A 194 "
       pdb=" CA  VAL A 194 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.18e-02 7.18e+03 9.66e+00
  bond pdb=" N   VAL B 194 "
       pdb=" CA  VAL B 194 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.18e-02 7.18e+03 9.66e+00
  bond pdb=" N   HIS B  72 "
       pdb=" CA  HIS B  72 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.18e-02 7.18e+03 8.92e+00
  bond pdb=" N   HIS A  72 "
       pdb=" CA  HIS A  72 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.18e-02 7.18e+03 8.92e+00
  bond pdb=" N   ILE A  73 "
       pdb=" CA  ILE A  73 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.70e+00
  ... (remaining 4967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 6328
        1.58 -     3.16: 326
        3.16 -     4.74: 54
        4.74 -     6.32: 28
        6.32 -     7.90: 4
  Bond angle restraints: 6740
  Sorted by residual:
  angle pdb=" C   TYR A  77 "
        pdb=" N   ARG A  78 "
        pdb=" CA  ARG A  78 "
      ideal   model   delta    sigma   weight residual
     122.08  127.51   -5.43 1.47e+00 4.63e-01 1.37e+01
  angle pdb=" C   TYR B  77 "
        pdb=" N   ARG B  78 "
        pdb=" CA  ARG B  78 "
      ideal   model   delta    sigma   weight residual
     122.08  127.51   -5.43 1.47e+00 4.63e-01 1.37e+01
  angle pdb=" C   GLU B 249 "
        pdb=" N   ASN B 250 "
        pdb=" CA  ASN B 250 "
      ideal   model   delta    sigma   weight residual
     122.46  127.15   -4.69 1.41e+00 5.03e-01 1.11e+01
  angle pdb=" C   GLU A 249 "
        pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
      ideal   model   delta    sigma   weight residual
     122.46  127.15   -4.69 1.41e+00 5.03e-01 1.11e+01
  angle pdb=" CA  ILE B  73 "
        pdb=" C   ILE B  73 "
        pdb=" O   ILE B  73 "
      ideal   model   delta    sigma   weight residual
     120.95  117.51    3.44 1.04e+00 9.25e-01 1.09e+01
  ... (remaining 6735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.97: 2532
       14.97 -    29.95: 302
       29.95 -    44.92: 106
       44.92 -    59.89: 12
       59.89 -    74.86: 14
  Dihedral angle restraints: 2966
    sinusoidal: 1164
      harmonic: 1802
  Sorted by residual:
  dihedral pdb=" CA  ASN B 154 "
           pdb=" C   ASN B 154 "
           pdb=" N   VAL B 155 "
           pdb=" CA  VAL B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.27  -29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  ASN A 154 "
           pdb=" C   ASN A 154 "
           pdb=" N   VAL A 155 "
           pdb=" CA  VAL A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.27  -29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  GLU B 328 "
           pdb=" C   GLU B 328 "
           pdb=" N   VAL B 329 "
           pdb=" CA  VAL B 329 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 2963 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 442
       0.040 -    0.079: 242
       0.079 -    0.118: 54
       0.118 -    0.158: 16
       0.158 -    0.197: 8
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  LEU A 198 "
            pdb=" N   LEU A 198 "
            pdb=" C   LEU A 198 "
            pdb=" CB  LEU A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  LEU B 198 "
            pdb=" N   LEU B 198 "
            pdb=" C   LEU B 198 "
            pdb=" CB  LEU B 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CA  ARG B  71 "
            pdb=" N   ARG B  71 "
            pdb=" C   ARG B  71 "
            pdb=" CB  ARG B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.71e-01
  ... (remaining 759 not shown)

  Planarity restraints: 854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 263 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO B 264 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 264 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 264 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 263 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 264 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 264 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 264 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 172 "    0.036 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO B 173 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "    0.030 5.00e-02 4.00e+02
  ... (remaining 851 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1064
        2.77 -     3.30: 4390
        3.30 -     3.84: 7845
        3.84 -     4.37: 9309
        4.37 -     4.90: 15438
  Nonbonded interactions: 38046
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 197 "
            pdb=" CG  ARG A 310 "
     model   vdw
     2.241 3.520
  nonbonded pdb=" NH2 ARG B 197 "
            pdb=" CG  ARG B 310 "
     model   vdw
     2.241 3.520
  nonbonded pdb=" OE1 GLU B 246 "
            pdb=" OG1 THR B 256 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLU A 246 "
            pdb=" OG1 THR A 256 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   LEU B  99 "
            pdb=" OG  SER B 102 "
     model   vdw
     2.365 3.040
  ... (remaining 38041 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.010
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.460
  Find NCS groups from input model:        0.030
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
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      :  0.006   0.099   4972  Z= 0.320
  Angle     :  0.862   7.903   6740  Z= 0.489
  Chirality :  0.051   0.197    762
  Planarity :  0.006   0.063    854
  Dihedral  : 15.613  74.864   1806
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 10.85 %
    Favored  : 88.76 %
  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 aren not related in a simple way.
  whole: -5.38 (0.24), residues: 596
  helix: -4.27 (0.12), residues: 348
  sheet: -2.93 (0.62), residues: 36
  loop : -1.91 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 169 
 TYR   0.007   0.001   TYR A 107 
 PHE   0.009   0.002   PHE B 117 
 TRP   0.013   0.002   TRP B 119 
 HIS   0.002   0.001   HIS A   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 4972)
  covalent geometry    : angle       0.86208 ( 6740)
  hydrogen bonds       : bond        0.28433 (  204)
  hydrogen bonds       : angle      11.29549 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 162
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6621 (m-70) cc_final: 0.6383 (m90)
REVERT: A  132 ILE cc_start: 0.8956 (pt) cc_final: 0.8731 (pt)
REVERT: A  223 ASP cc_start: 0.6769 (m-30) cc_final: 0.6561 (m-30)
REVERT: A  269 PHE cc_start: 0.8515 (t80) cc_final: 0.7921 (t80)
REVERT: A  310 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7159 (mmm-85)
REVERT: B   42 HIS cc_start: 0.6619 (m-70) cc_final: 0.6381 (m90)
REVERT: B  132 ILE cc_start: 0.8957 (pt) cc_final: 0.8731 (pt)
REVERT: B  223 ASP cc_start: 0.6768 (m-30) cc_final: 0.6556 (m-30)
REVERT: B  269 PHE cc_start: 0.8517 (t80) cc_final: 0.7924 (t80)
REVERT: B  310 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7159 (mmm-85)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0713
  time to fit residues: 14.7449
Evaluate side-chains
  116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
A  61 ASN
A  74 HIS
A 131 ASN
A 154 ASN
A 157 HIS
A 218 ASN
A 273 GLN
A 307 ASN
B   7 HIS
B  61 ASN
B  74 HIS
B 131 ASN
B 154 ASN
B 157 HIS
B 218 ASN
B 273 GLN
B 307 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.154546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126469 restraints weight = 7953.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.129829 restraints weight = 4852.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.132137 restraints weight = 3568.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.133470 restraints weight = 2929.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.134627 restraints weight = 2580.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4972  Z= 0.138
  Angle     :  0.626   6.289   6740  Z= 0.311
  Chirality :  0.041   0.131    762
  Planarity :  0.005   0.042    854
  Dihedral  :  4.861  25.768    684
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.77 %
    Favored  : 77.91 %
  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 aren not related in a simple way.
  whole: -3.79 (0.29), residues: 596
  helix: -2.56 (0.21), residues: 378
  sheet: -2.58 (0.67), residues: 42
  loop : -1.78 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.011   0.001   TYR B 199 
 PHE   0.026   0.002   PHE B 221 
 TRP   0.009   0.002   TRP B  34 
 HIS   0.002   0.001   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4972)
  covalent geometry    : angle       0.62641 ( 6740)
  hydrogen bonds       : bond        0.03884 (  204)
  hydrogen bonds       : angle       5.49043 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6612 (m-70) cc_final: 0.6406 (m90)
REVERT: A  269 PHE cc_start: 0.8416 (t80) cc_final: 0.7970 (t80)
REVERT: B   42 HIS cc_start: 0.6607 (m-70) cc_final: 0.6399 (m90)
REVERT: B  269 PHE cc_start: 0.8408 (t80) cc_final: 0.7968 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 132
  average time/residue: 0.0538
  time to fit residues: 9.6289
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  283 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  61 ASN
B   3 HIS
B  61 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.152588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.124288 restraints weight = 7994.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.127604 restraints weight = 5012.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.129860 restraints weight = 3749.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.131148 restraints weight = 3095.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.132287 restraints weight = 2744.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4972  Z= 0.167
  Angle     :  0.650   7.741   6740  Z= 0.310
  Chirality :  0.042   0.125    762
  Planarity :  0.004   0.037    854
  Dihedral  :  4.691  25.458    684
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.03 %
    Favored  : 71.32 %
  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 aren not related in a simple way.
  whole: -2.98 (0.32), residues: 596
  helix: -1.79 (0.24), residues: 382
  sheet: -2.45 (0.60), residues: 50
  loop : -1.69 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 180 
 TYR   0.007   0.001   TYR A  77 
 PHE   0.014   0.002   PHE A 221 
 TRP   0.006   0.001   TRP A  34 
 HIS   0.004   0.001   HIS A   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4972)
  covalent geometry    : angle       0.64985 ( 6740)
  hydrogen bonds       : bond        0.03496 (  204)
  hydrogen bonds       : angle       5.07001 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6627 (m-70) cc_final: 0.6427 (m90)
REVERT: A  269 PHE cc_start: 0.8454 (t80) cc_final: 0.8019 (t80)
REVERT: B   42 HIS cc_start: 0.6623 (m-70) cc_final: 0.6422 (m90)
REVERT: B  269 PHE cc_start: 0.8450 (t80) cc_final: 0.8016 (t80)
  outliers start: 24
  outliers final: 12
  residues processed: 122
  average time/residue: 0.0599
  time to fit residues: 9.4497
Evaluate side-chains
  116 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0970
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
B   3 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.155696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.128173 restraints weight = 7950.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131348 restraints weight = 5073.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133679 restraints weight = 3808.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.135216 restraints weight = 3134.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136147 restraints weight = 2742.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4972  Z= 0.107
  Angle     :  0.604   7.855   6740  Z= 0.276
  Chirality :  0.039   0.126    762
  Planarity :  0.003   0.032    854
  Dihedral  :  4.299  22.954    684
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.42 %
    Favored  : 71.71 %
  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 aren not related in a simple way.
  whole: -2.22 (0.33), residues: 596
  helix: -1.01 (0.27), residues: 374
  sheet: -2.75 (0.78), residues: 36
  loop : -1.85 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.009   0.001   TYR B 199 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.005   0.001   TRP A  34 
 HIS   0.004   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4972)
  covalent geometry    : angle       0.60369 ( 6740)
  hydrogen bonds       : bond        0.02858 (  204)
  hydrogen bonds       : angle       4.50371 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8392 (t80) cc_final: 0.7922 (t80)
REVERT: B  269 PHE cc_start: 0.8391 (t80) cc_final: 0.7924 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 134
  average time/residue: 0.0500
  time to fit residues: 8.9579
Evaluate side-chains
  124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 HIS
Chi-restraints excluded: chain A residue   74 HIS
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue    3 HIS
Chi-restraints excluded: chain B residue   74 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4076 r_free = 0.4076 target = 0.155750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.127253 restraints weight = 8105.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.130741 restraints weight = 4959.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133170 restraints weight = 3646.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.134784 restraints weight = 2981.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.135848 restraints weight = 2606.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4972  Z= 0.109
  Angle     :  0.591   6.693   6740  Z= 0.273
  Chirality :  0.040   0.121    762
  Planarity :  0.003   0.032    854
  Dihedral  :  4.235  22.720    684
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 26.36 %
    Favored  : 68.60 %
  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 aren not related in a simple way.
  whole: -1.77 (0.34), residues: 596
  helix: -0.55 (0.28), residues: 372
  sheet: -2.20 (1.01), residues: 26
  loop : -2.04 (0.39), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.009   0.001   TYR B 199 
 PHE   0.012   0.001   PHE A 117 
 TRP   0.004   0.001   TRP A 119 
 HIS   0.009   0.001   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4972)
  covalent geometry    : angle       0.59126 ( 6740)
  hydrogen bonds       : bond        0.02809 (  204)
  hydrogen bonds       : angle       4.38924 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8404 (t80) cc_final: 0.7967 (t80)
REVERT: B  269 PHE cc_start: 0.8404 (t80) cc_final: 0.7967 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 140
  average time/residue: 0.0525
  time to fit residues: 9.8506
Evaluate side-chains
  130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** 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 = 0.4074 r_free = 0.4074 target = 0.155396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126872 restraints weight = 8131.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.130391 restraints weight = 4957.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.132857 restraints weight = 3645.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.134536 restraints weight = 2970.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135316 restraints weight = 2582.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4972  Z= 0.116
  Angle     :  0.586   6.234   6740  Z= 0.274
  Chirality :  0.040   0.158    762
  Planarity :  0.003   0.030    854
  Dihedral  :  4.142  22.521    684
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 26.36 %
    Favored  : 67.83 %
  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 aren not related in a simple way.
  whole: -1.52 (0.34), residues: 596
  helix: -0.28 (0.28), residues: 372
  sheet: -2.31 (0.64), residues: 52
  loop : -1.93 (0.44), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 180 
 TYR   0.009   0.001   TYR B 199 
 PHE   0.010   0.001   PHE A 221 
 TRP   0.003   0.001   TRP A 119 
 HIS   0.001   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4972)
  covalent geometry    : angle       0.58630 ( 6740)
  hydrogen bonds       : bond        0.02692 (  204)
  hydrogen bonds       : angle       4.31642 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  260 GLU cc_start: 0.8018 (pp20) cc_final: 0.7647 (pp20)
REVERT: A  269 PHE cc_start: 0.8404 (t80) cc_final: 0.8034 (t80)
REVERT: B  260 GLU cc_start: 0.8020 (pp20) cc_final: 0.7645 (pp20)
REVERT: B  269 PHE cc_start: 0.8403 (t80) cc_final: 0.8035 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 146
  average time/residue: 0.0527
  time to fit residues: 10.3387
Evaluate side-chains
  134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0030
   chunk 19 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0060
   chunk 1 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.5006

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.156757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.129489 restraints weight = 7958.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.132759 restraints weight = 5057.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.135029 restraints weight = 3778.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.136526 restraints weight = 3105.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.137496 restraints weight = 2719.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4972  Z= 0.097
  Angle     :  0.575   7.099   6740  Z= 0.263
  Chirality :  0.039   0.132    762
  Planarity :  0.004   0.043    854
  Dihedral  :  4.000  21.656    684
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 27.13 %
    Favored  : 67.05 %
  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 aren not related in a simple way.
  whole: -1.09 (0.35), residues: 596
  helix:  0.05 (0.28), residues: 374
  sheet: -2.21 (1.03), residues: 26
  loop : -1.90 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 180 
 TYR   0.007   0.001   TYR A 274 
 PHE   0.007   0.001   PHE A 221 
 TRP   0.003   0.001   TRP B  82 
 HIS   0.001   0.000   HIS A   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4972)
  covalent geometry    : angle       0.57520 ( 6740)
  hydrogen bonds       : bond        0.02550 (  204)
  hydrogen bonds       : angle       4.17277 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  260 GLU cc_start: 0.7941 (pp20) cc_final: 0.7723 (pp20)
REVERT: B  260 GLU cc_start: 0.7941 (pp20) cc_final: 0.7724 (pp20)
  outliers start: 30
  outliers final: 24
  residues processed: 146
  average time/residue: 0.0550
  time to fit residues: 10.5420
Evaluate side-chains
  144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0270
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0670
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.3580

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 ASN
A 273 GLN
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 ASN
B 273 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.153199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.124890 restraints weight = 8152.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.128338 restraints weight = 4905.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.130633 restraints weight = 3597.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.132154 restraints weight = 2948.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.133171 restraints weight = 2585.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4972  Z= 0.168
  Angle     :  0.660   7.505   6740  Z= 0.313
  Chirality :  0.042   0.138    762
  Planarity :  0.004   0.041    854
  Dihedral  :  4.301  23.621    684
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 29.07 %
    Favored  : 65.12 %
  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 aren not related in a simple way.
  whole: -1.15 (0.35), residues: 596
  helix: -0.01 (0.28), residues: 374
  sheet: -2.83 (0.60), residues: 48
  loop : -1.55 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.013   0.001   TYR B 199 
 PHE   0.005   0.001   PHE A 221 
 TRP   0.004   0.001   TRP A 119 
 HIS   0.002   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 4972)
  covalent geometry    : angle       0.65965 ( 6740)
  hydrogen bonds       : bond        0.03073 (  204)
  hydrogen bonds       : angle       4.61203 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8494 (t80) cc_final: 0.8121 (t80)
REVERT: B  269 PHE cc_start: 0.8496 (t80) cc_final: 0.8125 (t80)
  outliers start: 30
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0487
  time to fit residues: 8.3969
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  283 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0870
   chunk 25 optimal weight:    0.0470
   chunk 58 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.4856

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** 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 = 0.4086 r_free = 0.4086 target = 0.156674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.128772 restraints weight = 8075.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.132060 restraints weight = 5179.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.134299 restraints weight = 3881.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135821 restraints weight = 3213.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.136694 restraints weight = 2826.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4972  Z= 0.099
  Angle     :  0.605   7.199   6740  Z= 0.281
  Chirality :  0.039   0.144    762
  Planarity :  0.003   0.030    854
  Dihedral  :  4.030  21.822    684
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 29.84 %
    Favored  : 65.89 %
  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 aren not related in a simple way.
  whole: -0.87 (0.35), residues: 596
  helix:  0.27 (0.29), residues: 374
  sheet: -2.49 (0.64), residues: 52
  loop : -1.64 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 180 
 TYR   0.006   0.001   TYR B 199 
 PHE   0.008   0.001   PHE A 221 
 TRP   0.004   0.001   TRP A  82 
 HIS   0.001   0.000   HIS B   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4972)
  covalent geometry    : angle       0.60457 ( 6740)
  hydrogen bonds       : bond        0.02713 (  204)
  hydrogen bonds       : angle       4.28146 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.186 
Fit side-chains
  outliers start: 22
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0557
  time to fit residues: 9.5110
Evaluate side-chains
  126 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** 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 = 0.4070 r_free = 0.4070 target = 0.155387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.127172 restraints weight = 8104.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.130358 restraints weight = 5182.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.132608 restraints weight = 3915.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.133910 restraints weight = 3253.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.135081 restraints weight = 2886.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4972  Z= 0.133
  Angle     :  0.653   7.158   6740  Z= 0.314
  Chirality :  0.042   0.203    762
  Planarity :  0.004   0.041    854
  Dihedral  :  4.191  22.341    684
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 31.78 %
    Favored  : 64.34 %
  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 aren not related in a simple way.
  whole: -0.79 (0.35), residues: 596
  helix:  0.30 (0.28), residues: 376
  sheet: -2.71 (0.61), residues: 48
  loop : -1.48 (0.47), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.007   0.001   TYR A 274 
 PHE   0.010   0.001   PHE A 117 
 TRP   0.002   0.001   TRP A  82 
 HIS   0.001   0.000   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4972)
  covalent geometry    : angle       0.65349 ( 6740)
  hydrogen bonds       : bond        0.03236 (  204)
  hydrogen bonds       : angle       4.34690 (  612)

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

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

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1192 Ramachandran restraints generated.
    596 Oldfield, 0 Emsley, 596 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8440 (t80) cc_final: 0.8038 (t80)
REVERT: B  269 PHE cc_start: 0.8436 (t80) cc_final: 0.8036 (t80)
  outliers start: 20
  outliers final: 18
  residues processed: 120
  average time/residue: 0.0482
  time to fit residues: 7.7526
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  150 LYS
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0370
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** 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 = 0.4082 r_free = 0.4082 target = 0.156310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.128524 restraints weight = 8027.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131710 restraints weight = 5130.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133918 restraints weight = 3857.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.135173 restraints weight = 3190.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.136341 restraints weight = 2824.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4972  Z= 0.119
  Angle     :  0.682   7.917   6740  Z= 0.331
  Chirality :  0.042   0.214    762
  Planarity :  0.004   0.057    854
  Dihedral  :  4.159  22.219    684
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 32.56 %
    Favored  : 63.57 %
  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 aren not related in a simple way.
  whole: -0.73 (0.35), residues: 596
  helix:  0.30 (0.28), residues: 374
  sheet: -2.53 (0.61), residues: 48
  loop : -1.38 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 180 
 TYR   0.006   0.001   TYR A 274 
 PHE   0.019   0.002   PHE A 117 
 TRP   0.003   0.001   TRP B  82 
 HIS   0.001   0.000   HIS A   3 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4972)
  covalent geometry    : angle       0.68178 ( 6740)
  hydrogen bonds       : bond        0.03010 (  204)
  hydrogen bonds       : angle       4.36123 (  612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 914.88 seconds
wall clock time: 16 minutes 27.82 seconds (987.82 seconds total)