Starting phenix.real_space_refine
on Sat May 10 04:13:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gsz_34244/05_2025/8gsz_34244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gsz_34244/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gsz_34244/05_2025/8gsz_34244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gsz_34244/05_2025/8gsz_34244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gsz_34244/05_2025/8gsz_34244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gsz_34244/05_2025/8gsz_34244.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.98, per 1000 atoms: 0.82
  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: 1.19
  Conformation dependent library (CDL) restraints added in 556.4 milliseconds
  

  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: 0.54
  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: 1.15

  Time building geometry restraints manager: 1.38 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: 0.02
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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.580
  Find NCS groups from input model:        0.060
  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:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.590
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.002   TRP B 119 
 HIS   0.002   0.001   HIS A   7 
 PHE   0.009   0.002   PHE B 117 
 TYR   0.007   0.001   TYR A 107 
 ARG   0.001   0.000   ARG A 169 

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

*********************** 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  : 0.528 
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: 0.1772
  time to fit residues: 36.0485
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  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.155232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.127300 restraints weight = 7826.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.130670 restraints weight = 4792.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132974 restraints weight = 3532.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4972  Z= 0.127
  Angle     :  0.619   6.330   6740  Z= 0.306
  Chirality :  0.041   0.130    762
  Planarity :  0.005   0.041    854
  Dihedral  :  4.833  25.615    684
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.38 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.29), residues: 596
  helix: -2.57 (0.21), residues: 378
  sheet: -2.61 (0.66), residues: 42
  loop : -1.80 (0.44), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  34 
 HIS   0.002   0.001   HIS A 332 
 PHE   0.024   0.002   PHE B 221 
 TYR   0.011   0.001   TYR A 199 
 ARG   0.003   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03991 (  204)
  hydrogen bonds       : angle       5.50732 (  612)
  covalent geometry    : bond        0.00286 ( 4972)
  covalent geometry    : angle       0.61927 ( 6740)

*********************** 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
  138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   42 HIS cc_start: 0.6635 (m-70) cc_final: 0.6431 (m90)
REVERT: A  199 TYR cc_start: 0.7813 (m-80) cc_final: 0.7600 (m-80)
REVERT: A  269 PHE cc_start: 0.8381 (t80) cc_final: 0.7932 (t80)
REVERT: B   42 HIS cc_start: 0.6631 (m-70) cc_final: 0.6428 (m90)
REVERT: B  199 TYR cc_start: 0.7804 (m-80) cc_final: 0.7593 (m-80)
REVERT: B  269 PHE cc_start: 0.8376 (t80) cc_final: 0.7929 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 132
  average time/residue: 0.1407
  time to fit residues: 24.6178
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  283 ASP
Chi-restraints excluded: chain B residue   48 VAL
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 50 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.149559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.121084 restraints weight = 7991.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.124195 restraints weight = 5101.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.126332 restraints weight = 3857.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087   4972  Z= 0.247
  Angle     :  0.723   6.087   6740  Z= 0.351
  Chirality :  0.045   0.147    762
  Planarity :  0.004   0.041    854
  Dihedral  :  4.978  26.975    684
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 22.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.32), residues: 596
  helix: -1.90 (0.24), residues: 378
  sheet: -2.53 (0.60), residues: 50
  loop : -1.54 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 119 
 HIS   0.004   0.001   HIS A   3 
 PHE   0.012   0.002   PHE B 221 
 TYR   0.013   0.001   TYR B 199 
 ARG   0.004   0.001   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  204)
  hydrogen bonds       : angle       5.42917 (  612)
  covalent geometry    : bond        0.00578 ( 4972)
  covalent geometry    : angle       0.72268 ( 6740)

*********************** 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
  134 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8551 (t80) cc_final: 0.8213 (t80)
REVERT: B  269 PHE cc_start: 0.8549 (t80) cc_final: 0.8212 (t80)
  outliers start: 32
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1408
  time to fit residues: 23.0292
Evaluate side-chains
  112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
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   63 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  72 HIS
B   3 HIS
B  72 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.153682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125672 restraints weight = 8041.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.129078 restraints weight = 5033.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131289 restraints weight = 3745.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4972  Z= 0.124
  Angle     :  0.627   7.725   6740  Z= 0.289
  Chirality :  0.040   0.119    762
  Planarity :  0.003   0.035    854
  Dihedral  :  4.465  23.948    684
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 23.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.33), residues: 596
  helix: -1.21 (0.26), residues: 374
  sheet: -2.98 (0.71), residues: 42
  loop : -1.77 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B   3 
 PHE   0.010   0.001   PHE A 117 
 TYR   0.007   0.001   TYR B 274 
 ARG   0.004   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (  204)
  hydrogen bonds       : angle       4.69507 (  612)
  covalent geometry    : bond        0.00299 ( 4972)
  covalent geometry    : angle       0.62680 ( 6740)

*********************** 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
  148 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  269 PHE cc_start: 0.8480 (t80) cc_final: 0.8064 (t80)
REVERT: B  269 PHE cc_start: 0.8476 (t80) cc_final: 0.8074 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 130
  average time/residue: 0.1522
  time to fit residues: 25.6381
Evaluate side-chains
  122 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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  194 VAL
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  273 GLN
Chi-restraints excluded: chain A residue  283 ASP
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  194 VAL
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  273 GLN
Chi-restraints excluded: chain B residue  283 ASP
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 52 optimal weight:    0.0770
   chunk 60 optimal weight:    0.0670
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.156113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.127760 restraints weight = 8102.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131331 restraints weight = 4944.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.133819 restraints weight = 3636.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4972  Z= 0.099
  Angle     :  0.605   7.050   6740  Z= 0.273
  Chirality :  0.039   0.145    762
  Planarity :  0.003   0.032    854
  Dihedral  :  4.276  22.604    684
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.34), residues: 596
  helix: -0.59 (0.27), residues: 372
  sheet: -2.97 (0.80), residues: 36
  loop : -1.90 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 119 
 HIS   0.008   0.001   HIS B   3 
 PHE   0.012   0.001   PHE A 117 
 TYR   0.008   0.001   TYR A  81 
 ARG   0.002   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02778 (  204)
  hydrogen bonds       : angle       4.42051 (  612)
  covalent geometry    : bond        0.00235 ( 4972)
  covalent geometry    : angle       0.60460 ( 6740)

*********************** 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  : 0.565 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7802 (m-80) cc_final: 0.7481 (m-80)
REVERT: A  252 GLN cc_start: 0.6147 (mm110) cc_final: 0.5843 (mm110)
REVERT: A  269 PHE cc_start: 0.8461 (t80) cc_final: 0.8069 (t80)
REVERT: B   81 TYR cc_start: 0.7804 (m-80) cc_final: 0.7485 (m-80)
REVERT: B  252 GLN cc_start: 0.6144 (mm110) cc_final: 0.5841 (mm110)
REVERT: B  269 PHE cc_start: 0.8450 (t80) cc_final: 0.8017 (t80)
  outliers start: 26
  outliers final: 22
  residues processed: 140
  average time/residue: 0.1555
  time to fit residues: 28.5368
Evaluate side-chains
  140 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   74 HIS
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  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   74 HIS
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0060
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    7.9990
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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  72 HIS
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.155290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.126852 restraints weight = 8005.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.130330 restraints weight = 4959.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.132737 restraints weight = 3679.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3759

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= 0.115
  Angle     :  0.598   7.058   6740  Z= 0.277
  Chirality :  0.040   0.155    762
  Planarity :  0.003   0.031    854
  Dihedral  :  4.168  22.449    684
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.34), residues: 596
  helix: -0.24 (0.28), residues: 372
  sheet: -2.97 (0.81), residues: 36
  loop : -1.84 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 119 
 HIS   0.002   0.000   HIS B   3 
 PHE   0.007   0.001   PHE A 221 
 TYR   0.008   0.001   TYR B 274 
 ARG   0.001   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02694 (  204)
  hydrogen bonds       : angle       4.34040 (  612)
  covalent geometry    : bond        0.00278 ( 4972)
  covalent geometry    : angle       0.59815 ( 6740)

*********************** 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  : 0.523 
Fit side-chains
REVERT: A   81 TYR cc_start: 0.7828 (m-80) cc_final: 0.7472 (m-80)
REVERT: A  106 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.5019 (t80)
REVERT: A  252 GLN cc_start: 0.6297 (mm110) cc_final: 0.5961 (mm110)
REVERT: A  269 PHE cc_start: 0.8480 (t80) cc_final: 0.8132 (t80)
REVERT: B   81 TYR cc_start: 0.7825 (m-80) cc_final: 0.7470 (m-80)
REVERT: B  106 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.5022 (t80)
REVERT: B  252 GLN cc_start: 0.6292 (mm110) cc_final: 0.5956 (mm110)
REVERT: B  269 PHE cc_start: 0.8460 (t80) cc_final: 0.8119 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1522
  time to fit residues: 29.1556
Evaluate side-chains
  142 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
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  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  273 GLN
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   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
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  273 GLN
Chi-restraints excluded: chain B residue  285 LEU
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 20 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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  72 HIS
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.153702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.125438 restraints weight = 7946.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.128735 restraints weight = 5062.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.130899 restraints weight = 3809.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4972  Z= 0.146
  Angle     :  0.621   6.552   6740  Z= 0.288
  Chirality :  0.041   0.142    762
  Planarity :  0.004   0.036    854
  Dihedral  :  4.270  23.767    684
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 26.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.34), residues: 596
  helix: -0.14 (0.28), residues: 372
  sheet: -2.92 (0.95), residues: 22
  loop : -1.70 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 119 
 HIS   0.002   0.001   HIS B  72 
 PHE   0.006   0.001   PHE A 221 
 TYR   0.011   0.001   TYR B 199 
 ARG   0.003   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02769 (  204)
  hydrogen bonds       : angle       4.48046 (  612)
  covalent geometry    : bond        0.00353 ( 4972)
  covalent geometry    : angle       0.62085 ( 6740)

*********************** 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
  152 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A  252 GLN cc_start: 0.6222 (mm110) cc_final: 0.5900 (mm110)
REVERT: A  269 PHE cc_start: 0.8518 (t80) cc_final: 0.8173 (t80)
REVERT: B  252 GLN cc_start: 0.6220 (mm110) cc_final: 0.5899 (mm110)
REVERT: B  269 PHE cc_start: 0.8507 (t80) cc_final: 0.8190 (t80)
  outliers start: 32
  outliers final: 28
  residues processed: 137
  average time/residue: 0.1505
  time to fit residues: 26.8723
Evaluate side-chains
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
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  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  222 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  273 GLN
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  106 TYR
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  222 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  273 GLN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0470
   chunk 59 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4074

-------------------------------------------------------------------------------
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  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 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 = 0.4091 r_free = 0.4091 target = 0.156537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.128545 restraints weight = 8094.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132074 restraints weight = 4925.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.134345 restraints weight = 3614.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3958

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= 0.096
  Angle     :  0.589   6.526   6740  Z= 0.271
  Chirality :  0.039   0.137    762
  Planarity :  0.004   0.034    854
  Dihedral  :  4.080  21.630    684
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 28.29 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.35), residues: 596
  helix:  0.15 (0.28), residues: 374
  sheet: -2.20 (1.06), residues: 26
  loop : -1.80 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.006   0.001   PHE A 221 
 TYR   0.007   0.001   TYR B 274 
 ARG   0.003   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02614 (  204)
  hydrogen bonds       : angle       4.25145 (  612)
  covalent geometry    : bond        0.00225 ( 4972)
  covalent geometry    : angle       0.58921 ( 6740)

*********************** 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
  147 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 1.318 
Fit side-chains
REVERT: A  106 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.5168 (t80)
REVERT: A  269 PHE cc_start: 0.8443 (t80) cc_final: 0.8044 (t80)
REVERT: B  106 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.5173 (t80)
REVERT: B  269 PHE cc_start: 0.8434 (t80) cc_final: 0.8051 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1675
  time to fit residues: 29.3534
Evaluate side-chains
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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  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  273 GLN
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  106 TYR
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  273 GLN
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 57 optimal weight:    0.3980
   chunk 7 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 19 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 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 = 0.4080 r_free = 0.4080 target = 0.155689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.128295 restraints weight = 7964.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.131465 restraints weight = 5107.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133631 restraints weight = 3849.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4972  Z= 0.110
  Angle     :  0.615   6.312   6740  Z= 0.285
  Chirality :  0.040   0.144    762
  Planarity :  0.003   0.030    854
  Dihedral  :  4.069  21.664    684
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.07 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.35), residues: 596
  helix:  0.26 (0.28), residues: 374
  sheet: -3.33 (0.71), residues: 36
  loop : -1.48 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.009   0.001   PHE A 117 
 TYR   0.008   0.001   TYR A 274 
 ARG   0.007   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02624 (  204)
  hydrogen bonds       : angle       4.35269 (  612)
  covalent geometry    : bond        0.00263 ( 4972)
  covalent geometry    : angle       0.61459 ( 6740)

*********************** 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
  148 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A  106 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.5166 (t80)
REVERT: A  124 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7971 (mm)
REVERT: A  269 PHE cc_start: 0.8464 (t80) cc_final: 0.8048 (t80)
REVERT: B  106 TYR cc_start: 0.5370 (OUTLIER) cc_final: 0.5163 (t80)
REVERT: B  124 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7973 (mm)
REVERT: B  269 PHE cc_start: 0.8471 (t80) cc_final: 0.8102 (t80)
  outliers start: 28
  outliers final: 20
  residues processed: 134
  average time/residue: 0.1452
  time to fit residues: 25.3919
Evaluate side-chains
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
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  150 LYS
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  273 GLN
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   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
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  273 GLN
Chi-restraints excluded: chain B residue  285 LEU
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 46 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  72 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 = 0.4079 r_free = 0.4079 target = 0.155711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.127742 restraints weight = 8044.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.130955 restraints weight = 5202.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.132993 restraints weight = 3944.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4972  Z= 0.122
  Angle     :  0.624   6.842   6740  Z= 0.295
  Chirality :  0.041   0.176    762
  Planarity :  0.004   0.030    854
  Dihedral  :  4.145  22.161    684
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.65 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.35), residues: 596
  helix:  0.25 (0.28), residues: 374
  sheet: -2.93 (0.57), residues: 48
  loop : -1.49 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A  72 
 PHE   0.020   0.002   PHE A 117 
 TYR   0.007   0.001   TYR A 199 
 ARG   0.005   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02958 (  204)
  hydrogen bonds       : angle       4.41961 (  612)
  covalent geometry    : bond        0.00289 ( 4972)
  covalent geometry    : angle       0.62352 ( 6740)

********************** 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
  145 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  106 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.5157 (t80)
REVERT: A  124 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7945 (mm)
REVERT: A  269 PHE cc_start: 0.8476 (t80) cc_final: 0.8068 (t80)
REVERT: B  106 TYR cc_start: 0.5385 (OUTLIER) cc_final: 0.5159 (t80)
REVERT: B  124 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7950 (mm)
REVERT: B  269 PHE cc_start: 0.8482 (t80) cc_final: 0.8124 (t80)
  outliers start: 28
  outliers final: 22
  residues processed: 132
  average time/residue: 0.1441
  time to fit residues: 25.1934
Evaluate side-chains
  137 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
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  150 LYS
Chi-restraints excluded: chain A residue  210 ASP
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  271 MET
Chi-restraints excluded: chain A residue  273 GLN
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   99 LEU
Chi-restraints excluded: chain B residue  106 TYR
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  210 ASP
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  271 MET
Chi-restraints excluded: chain B residue  273 GLN
Chi-restraints excluded: chain B residue  285 LEU
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 29 optimal weight:    0.0070
   chunk 58 optimal weight:    0.0870
   chunk 14 optimal weight:    0.3980
   chunk 60 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.3176

-------------------------------------------------------------------------------
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  72 HIS
A 152 ASN
** B   3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  72 HIS
B 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.158724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.130671 restraints weight = 8021.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.134000 restraints weight = 5096.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.136387 restraints weight = 3825.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   4972  Z= 0.100
  Angle     :  0.649   6.740   6740  Z= 0.312
  Chirality :  0.039   0.183    762
  Planarity :  0.004   0.059    854
  Dihedral  :  4.015  20.339    684
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 33.53 %
    Favored  : 63.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.35), residues: 596
  helix:  0.22 (0.28), residues: 374
  sheet: -2.99 (0.73), residues: 40
  loop : -1.76 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A  72 
 PHE   0.020   0.002   PHE A 117 
 TYR   0.007   0.001   TYR B 274 
 ARG   0.024   0.001   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02623 (  204)
  hydrogen bonds       : angle       4.30908 (  612)
  covalent geometry    : bond        0.00233 ( 4972)
  covalent geometry    : angle       0.64938 ( 6740)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1977.97 seconds
wall clock time: 35 minutes 21.50 seconds (2121.50 seconds total)