Starting phenix.real_space_refine
on Wed Feb  4 02:26:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qvm_14180/02_2026/7qvm_14180.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    5450      2.51       5
     N    1438      2.21       5
     O    1575      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8528
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "L"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 68
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 1994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1994
          Classifications: {'peptide': 250}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 10, 'TRANS': 239}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "S"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1770
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.65, per 1000 atoms: 0.19
  Number of scatterers: 8528
  At special positions: 0
  Unit cell: (93.093, 122.388, 127.596, 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      65     16.00
     O    1575      8.00
     N    1438      7.00
     C    5450      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L   1 " - pdb=" SG  CYS L   6 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 112 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 332.2 milliseconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2054

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      37.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.754A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 5.098A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 4.024A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.863A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.551A  pdb=" N   ALA A 301 " --> pdb=" O   TYR A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 4.030A  pdb=" N   VAL A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.723A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 4.107A  pdb=" N   ARG G  13 " --> pdb=" O   ILE G   9 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 36 through 59
    Processing helix  chain 'R' and resid 60 through 65
      removed outlier: 3.654A  pdb=" N   ARG R  65 " --> pdb=" O   LEU R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 103
      removed outlier: 3.644A  pdb=" N   VAL R  93 " --> pdb=" O   ALA R  89 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU R  94 " --> pdb=" O   VAL R  90 " (cutoff:3.500A)
      Proline residue:  R  95  - end of helix
    Processing helix  chain 'R' and resid 108 through 143
      removed outlier: 3.858A  pdb=" N   THR R 127 " --> pdb=" O   MET R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 175
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 195 through 209
    Processing helix  chain 'R' and resid 209 through 230
    Processing helix  chain 'R' and resid 271 through 301
      Proline residue:  R 290  - end of helix
    Processing helix  chain 'R' and resid 308 through 317
      removed outlier: 3.795A  pdb=" N   LEU R 316 " --> pdb=" O   ILE R 312 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU R 317 " --> pdb=" O   ILE R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 319 through 333
      Proline residue:  R 326  - end of helix
      removed outlier: 3.567A  pdb=" N   THR R 333 " --> pdb=" O   TYR R 329 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 338
      removed outlier: 3.747A  pdb=" N   PHE R 337 " --> pdb=" O   THR R 333 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.532A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.568A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.843A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 72
      removed outlier: 6.469A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.797A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.158A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.299A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.885A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.778A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 4.107A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.885A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR S  50 " --> pdb=" O   TYR S  59 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12
      removed outlier: 4.321A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.962A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1209 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: 1.24

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2615
        1.34 -     1.46: 1454
        1.46 -     1.58: 4547
        1.58 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 8708
  Sorted by residual:
  bond pdb=" C   THR S  84 "
       pdb=" N   SER S  85 "
    ideal  model  delta    sigma   weight residual
    1.333  1.266  0.066 1.29e-02 6.01e+03 2.65e+01
  bond pdb=" N   ILE L   3 "
       pdb=" CA  ILE L   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.50e+00
  bond pdb=" N   GLN R  92 "
       pdb=" CA  GLN R  92 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.24e-02 6.50e+03 7.27e+00
  bond pdb=" N   LEU R 316 "
       pdb=" CA  LEU R 316 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.33e-02 5.65e+03 6.57e+00
  bond pdb=" N   GLN R 171 "
       pdb=" CA  GLN R 171 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.17e-02 7.31e+03 5.45e+00
  ... (remaining 8703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 11260
        1.31 -     2.62: 412
        2.62 -     3.93: 100
        3.93 -     5.24: 29
        5.24 -     6.56: 8
  Bond angle restraints: 11809
  Sorted by residual:
  angle pdb=" N   TYR L   2 "
        pdb=" CA  TYR L   2 "
        pdb=" C   TYR L   2 "
      ideal   model   delta    sigma   weight residual
     113.12  109.08    4.04 1.25e+00 6.40e-01 1.04e+01
  angle pdb=" N   ASP A   9 "
        pdb=" CA  ASP A   9 "
        pdb=" C   ASP A   9 "
      ideal   model   delta    sigma   weight residual
     111.07  107.76    3.31 1.07e+00 8.73e-01 9.59e+00
  angle pdb=" C   THR S  84 "
        pdb=" N   SER S  85 "
        pdb=" CA  SER S  85 "
      ideal   model   delta    sigma   weight residual
     122.63  127.03   -4.40 1.44e+00 4.82e-01 9.32e+00
  angle pdb=" N   MET A 249 "
        pdb=" CA  MET A 249 "
        pdb=" C   MET A 249 "
      ideal   model   delta    sigma   weight residual
     110.97  107.66    3.31 1.09e+00 8.42e-01 9.24e+00
  angle pdb=" CA  LEU L   8 "
        pdb=" C   LEU L   8 "
        pdb=" O   LEU L   8 "
      ideal   model   delta    sigma   weight residual
     121.20  118.17    3.03 1.04e+00 9.25e-01 8.50e+00
  ... (remaining 11804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4698
       17.96 -    35.92: 387
       35.92 -    53.88: 55
       53.88 -    71.84: 6
       71.84 -    89.80: 6
  Dihedral angle restraints: 5152
    sinusoidal: 1980
      harmonic: 3172
  Sorted by residual:
  dihedral pdb=" CB  CYS R 112 "
           pdb=" SG  CYS R 112 "
           pdb=" SG  CYS R 187 "
           pdb=" CB  CYS R 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.69   85.69     1      1.00e+01 1.00e-02 8.88e+01
  dihedral pdb=" CB  CYS L   1 "
           pdb=" SG  CYS L   1 "
           pdb=" SG  CYS L   6 "
           pdb=" CB  CYS L   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.07  -60.07     1      1.00e+01 1.00e-02 4.81e+01
  dihedral pdb=" CA  GLN S  82 "
           pdb=" C   GLN S  82 "
           pdb=" N   MET S  83 "
           pdb=" CA  MET S  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.76  -22.24     0      5.00e+00 4.00e-02 1.98e+01
  ... (remaining 5149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 895
       0.035 -    0.070: 312
       0.070 -    0.105: 94
       0.105 -    0.140: 41
       0.140 -    0.175: 9
  Chirality restraints: 1351
  Sorted by residual:
  chirality pdb=" CA  GLU G  17 "
            pdb=" N   GLU G  17 "
            pdb=" C   GLU G  17 "
            pdb=" CB  GLU G  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  MET A 249 "
            pdb=" N   MET A 249 "
            pdb=" C   MET A 249 "
            pdb=" CB  MET A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  LEU A 250 "
            pdb=" N   LEU A 250 "
            pdb=" C   LEU A 250 "
            pdb=" CB  LEU A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 1348 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 341 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.40e+00
        pdb=" C   ASP A 341 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASP A 341 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE A 342 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  82 "    0.005 2.00e-02 2.50e+03   1.30e-02 4.24e+00
        pdb=" CG  TRP B  82 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  82 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  82 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  82 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  82 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  82 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  82 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  82 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  82 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "    0.016 2.00e-02 2.50e+03   1.08e-02 2.92e+00
        pdb=" CG  TRP B  63 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 262
        2.70 -     3.25: 8817
        3.25 -     3.80: 13858
        3.80 -     4.35: 17167
        4.35 -     4.90: 29414
  Nonbonded interactions: 69518
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   ALA B 231 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.248 3.040
  ... (remaining 69513 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.830
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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      :  0.003   0.093   8713  Z= 0.208
  Angle     :  0.640   6.556  11817  Z= 0.359
  Chirality :  0.044   0.175   1351
  Planarity :  0.004   0.043   1486
  Dihedral  : 12.937  89.801   3086
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.27), residues: 1068
  helix:  1.70 (0.29), residues: 353
  sheet: -0.52 (0.32), residues: 241
  loop : -0.63 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 209 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.017   0.001   PHE S  68 
 TRP   0.029   0.002   TRP B  63 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8708)
  covalent geometry    : angle       0.64002 (11809)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       0.77098 (    8)
  hydrogen bonds       : bond        0.13286 (  430)
  hydrogen bonds       : angle       5.82794 ( 1209)
  Misc. bond           : bond        0.09320 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  189 HIS cc_start: 0.7168 (p90) cc_final: 0.6950 (p90)
REVERT: A  243 ARG cc_start: 0.8749 (ptp-110) cc_final: 0.8291 (ptp-110)
REVERT: A  249 MET cc_start: 0.8227 (tpt) cc_final: 0.7991 (tpp)
REVERT: B   23 LYS cc_start: 0.9109 (tppt) cc_final: 0.8810 (mtmm)
REVERT: B   63 TRP cc_start: 0.7775 (m100) cc_final: 0.7540 (m100)
REVERT: B  274 THR cc_start: 0.8341 (m) cc_final: 0.7836 (p)
REVERT: G   20 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8490 (pttm)
REVERT: G   41 CYS cc_start: 0.7026 (t) cc_final: 0.6760 (t)
REVERT: R   42 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8518 (mt-10)
REVERT: R   79 LYS cc_start: 0.8214 (tttt) cc_final: 0.7645 (mmmt)
REVERT: R   92 GLN cc_start: 0.7935 (tp40) cc_final: 0.7238 (tp-100)
REVERT: R  119 GLN cc_start: 0.5790 (mt0) cc_final: 0.5419 (mt0)
REVERT: R  275 LYS cc_start: 0.7453 (tttt) cc_final: 0.7212 (tttt)
REVERT: S   83 MET cc_start: 0.8025 (tpt) cc_final: 0.7554 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1021
  time to fit residues: 27.4354
Evaluate side-chains
  172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0270
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** R 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.124051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.088355 restraints weight = 17147.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 3.14
r_work: 0.3327 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8713  Z= 0.127
  Angle     :  0.587   6.353  11817  Z= 0.304
  Chirality :  0.042   0.150   1351
  Planarity :  0.004   0.045   1486
  Dihedral  :  4.187  20.577   1169
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.36 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.26), residues: 1068
  helix:  2.18 (0.28), residues: 354
  sheet: -0.43 (0.32), residues: 244
  loop : -0.72 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 209 
 TYR   0.014   0.001   TYR S 102 
 PHE   0.019   0.001   PHE S 200 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8708)
  covalent geometry    : angle       0.58735 (11809)
  SS BOND              : bond        0.00106 (    4)
  SS BOND              : angle       0.57487 (    8)
  hydrogen bonds       : bond        0.03653 (  430)
  hydrogen bonds       : angle       4.78055 ( 1209)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 190
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.8952 (ptp-110) cc_final: 0.8558 (ptp-110)
REVERT: A  246 GLU cc_start: 0.9230 (pt0) cc_final: 0.9004 (pt0)
REVERT: A  277 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8792 (mm-30)
REVERT: B   23 LYS cc_start: 0.9165 (tppt) cc_final: 0.8820 (mtpt)
REVERT: B  197 ARG cc_start: 0.8413 (mmm160) cc_final: 0.8197 (mmm160)
REVERT: G   18 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8449 (tp-100)
REVERT: G   20 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8484 (pttm)
REVERT: G   21 MET cc_start: 0.9374 (tpp) cc_final: 0.9066 (ttp)
REVERT: G   47 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8077 (tm-30)
REVERT: L    5 ASN cc_start: 0.9026 (p0) cc_final: 0.8202 (m110)
REVERT: R   42 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8605 (mt-10)
REVERT: R   79 LYS cc_start: 0.8099 (tttt) cc_final: 0.7602 (mmmt)
REVERT: R   92 GLN cc_start: 0.8355 (tp40) cc_final: 0.7789 (tp40)
REVERT: R  226 LYS cc_start: 0.6489 (tppt) cc_final: 0.6103 (mmtm)
REVERT: R  275 LYS cc_start: 0.7403 (tttt) cc_final: 0.7150 (tttt)
REVERT: R  332 PHE cc_start: 0.5256 (t80) cc_final: 0.4972 (t80)
REVERT: S   76 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8678 (mtmm)
REVERT: S   83 MET cc_start: 0.7867 (tpt) cc_final: 0.7582 (tpt)
  outliers start: 6
  outliers final: 4
  residues processed: 194
  average time/residue: 0.1112
  time to fit residues: 28.2893
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 161
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
R 230 ASN
S 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.123069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087794 restraints weight = 17116.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 3.11
r_work: 0.3313 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8713  Z= 0.130
  Angle     :  0.564   9.261  11817  Z= 0.291
  Chirality :  0.042   0.278   1351
  Planarity :  0.004   0.045   1486
  Dihedral  :  4.168  20.767   1169
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.94 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1068
  helix:  2.38 (0.28), residues: 353
  sheet: -0.29 (0.32), residues: 242
  loop : -0.79 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 209 
 TYR   0.012   0.001   TYR S 102 
 PHE   0.013   0.001   PHE S 200 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8708)
  covalent geometry    : angle       0.56402 (11809)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.59517 (    8)
  hydrogen bonds       : bond        0.03326 (  430)
  hydrogen bonds       : angle       4.55500 ( 1209)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.8987 (ptp-110) cc_final: 0.8627 (ptp-110)
REVERT: A  313 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6780 (mtm-85)
REVERT: B   23 LYS cc_start: 0.9186 (tppt) cc_final: 0.8832 (mtpt)
REVERT: G   13 ARG cc_start: 0.8968 (mpp-170) cc_final: 0.8752 (mtt90)
REVERT: G   18 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8435 (tp-100)
REVERT: G   20 LYS cc_start: 0.8971 (ptpp) cc_final: 0.8500 (pttm)
REVERT: G   41 CYS cc_start: 0.7250 (t) cc_final: 0.6999 (t)
REVERT: G   47 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8081 (tm-30)
REVERT: L    5 ASN cc_start: 0.8960 (p0) cc_final: 0.8144 (m110)
REVERT: R   42 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8650 (mt-10)
REVERT: R   78 MET cc_start: 0.7625 (mtp) cc_final: 0.7386 (ttt)
REVERT: R   79 LYS cc_start: 0.8119 (tttt) cc_final: 0.7577 (mmmt)
REVERT: R   92 GLN cc_start: 0.8362 (tp40) cc_final: 0.7508 (tp-100)
REVERT: R  119 GLN cc_start: 0.5311 (OUTLIER) cc_final: 0.4847 (mt0)
REVERT: R  226 LYS cc_start: 0.6465 (tppt) cc_final: 0.6151 (mmtm)
REVERT: R  275 LYS cc_start: 0.7462 (tttt) cc_final: 0.7257 (tttt)
REVERT: R  332 PHE cc_start: 0.5213 (t80) cc_final: 0.4985 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 190
  average time/residue: 0.0929
  time to fit residues: 23.5132
Evaluate side-chains
  172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  119 GLN
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  171 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 99 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.121929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.085946 restraints weight = 17237.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.13
r_work: 0.3278 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8713  Z= 0.154
  Angle     :  0.574   8.001  11817  Z= 0.296
  Chirality :  0.042   0.200   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.209  21.564   1169
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.86 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.27), residues: 1068
  helix:  2.30 (0.28), residues: 359
  sheet: -0.53 (0.31), residues: 266
  loop : -0.72 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 313 
 TYR   0.016   0.001   TYR A 297 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8708)
  covalent geometry    : angle       0.57419 (11809)
  SS BOND              : bond        0.00131 (    4)
  SS BOND              : angle       0.48075 (    8)
  hydrogen bonds       : bond        0.03346 (  430)
  hydrogen bonds       : angle       4.49709 ( 1209)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9032 (ptp-110) cc_final: 0.8678 (ptp-110)
REVERT: A  256 ASN cc_start: 0.8059 (m-40) cc_final: 0.7674 (t0)
REVERT: B   23 LYS cc_start: 0.9212 (tppt) cc_final: 0.9001 (tppt)
REVERT: G   18 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8331 (tp-100)
REVERT: G   20 LYS cc_start: 0.8988 (ptpp) cc_final: 0.8768 (ptpt)
REVERT: G   21 MET cc_start: 0.9370 (tpp) cc_final: 0.9051 (tmm)
REVERT: G   41 CYS cc_start: 0.7296 (t) cc_final: 0.7005 (t)
REVERT: G   47 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: R   78 MET cc_start: 0.7630 (mtp) cc_final: 0.7408 (ttt)
REVERT: R   79 LYS cc_start: 0.8127 (tttt) cc_final: 0.7634 (mmmt)
REVERT: R  226 LYS cc_start: 0.6422 (tppt) cc_final: 0.6122 (mmtm)
REVERT: R  275 LYS cc_start: 0.7490 (tttt) cc_final: 0.7259 (tttt)
  outliers start: 18
  outliers final: 12
  residues processed: 177
  average time/residue: 0.1175
  time to fit residues: 27.0424
Evaluate side-chains
  167 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  222 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 69 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0370
   chunk 27 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 71 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.123400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.087714 restraints weight = 17147.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 3.13
r_work: 0.3313 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8713  Z= 0.112
  Angle     :  0.558   7.722  11817  Z= 0.288
  Chirality :  0.041   0.179   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.066  20.460   1169
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.61 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1068
  helix:  2.29 (0.28), residues: 359
  sheet: -0.32 (0.32), residues: 248
  loop : -0.74 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 197 
 TYR   0.027   0.001   TYR A 303 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8708)
  covalent geometry    : angle       0.55801 (11809)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.38059 (    8)
  hydrogen bonds       : bond        0.03186 (  430)
  hydrogen bonds       : angle       4.40420 ( 1209)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 169
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9037 (ptp-110) cc_final: 0.8656 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9200 (tppt) cc_final: 0.8965 (tppt)
REVERT: B  118 ASP cc_start: 0.8330 (m-30) cc_final: 0.8106 (m-30)
REVERT: G   18 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8298 (tp-100)
REVERT: G   21 MET cc_start: 0.9377 (tpp) cc_final: 0.9072 (tmm)
REVERT: G   41 CYS cc_start: 0.7275 (t) cc_final: 0.6984 (t)
REVERT: G   47 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: R   78 MET cc_start: 0.7586 (mtp) cc_final: 0.7372 (ttt)
REVERT: R   79 LYS cc_start: 0.8153 (tttt) cc_final: 0.7656 (mmmt)
REVERT: R   92 GLN cc_start: 0.8172 (tp40) cc_final: 0.7452 (tp-100)
REVERT: R  226 LYS cc_start: 0.6361 (tppt) cc_final: 0.6069 (mmtm)
REVERT: R  275 LYS cc_start: 0.7488 (tttt) cc_final: 0.7197 (tttt)
REVERT: S  208 GLU cc_start: 0.7832 (pm20) cc_final: 0.7631 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 179
  average time/residue: 0.0978
  time to fit residues: 23.0852
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 156
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  300 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 35 optimal weight:    0.2980
   chunk 55 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.119741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.085717 restraints weight = 16874.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.04
r_work: 0.3289 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8713  Z= 0.179
  Angle     :  0.590   7.217  11817  Z= 0.308
  Chirality :  0.043   0.188   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.278  21.778   1169
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.12 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.27), residues: 1068
  helix:  2.24 (0.28), residues: 359
  sheet: -0.51 (0.30), residues: 266
  loop : -0.72 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 197 
 TYR   0.020   0.002   TYR A 303 
 PHE   0.013   0.002   PHE B 199 
 TRP   0.038   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8708)
  covalent geometry    : angle       0.59034 (11809)
  SS BOND              : bond        0.00163 (    4)
  SS BOND              : angle       0.46604 (    8)
  hydrogen bonds       : bond        0.03461 (  430)
  hydrogen bonds       : angle       4.45619 ( 1209)
  Misc. bond           : bond        0.00020 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 158
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9046 (ptp-110) cc_final: 0.8665 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9227 (tppt) cc_final: 0.8987 (tppt)
REVERT: B  118 ASP cc_start: 0.8420 (m-30) cc_final: 0.8158 (m-30)
REVERT: G   18 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8271 (tp-100)
REVERT: G   20 LYS cc_start: 0.9124 (ptmt) cc_final: 0.8900 (ptpp)
REVERT: G   41 CYS cc_start: 0.7405 (t) cc_final: 0.6941 (t)
REVERT: G   47 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: R   78 MET cc_start: 0.7587 (mtp) cc_final: 0.7373 (ttt)
REVERT: R   79 LYS cc_start: 0.8158 (tttt) cc_final: 0.7657 (mmmt)
REVERT: R   92 GLN cc_start: 0.8253 (tp40) cc_final: 0.7509 (tp-100)
REVERT: R  226 LYS cc_start: 0.6415 (tppt) cc_final: 0.6134 (mmtm)
REVERT: R  275 LYS cc_start: 0.7528 (tttt) cc_final: 0.7297 (tttt)
  outliers start: 20
  outliers final: 14
  residues processed: 171
  average time/residue: 0.0988
  time to fit residues: 22.1375
Evaluate side-chains
  165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 151
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  288 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  222 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 86 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   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 307 GLN
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.122313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.086531 restraints weight = 17202.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 3.22
r_work: 0.3283 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8713  Z= 0.130
  Angle     :  0.599  10.691  11817  Z= 0.309
  Chirality :  0.042   0.191   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.186  21.019   1169
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.20 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.27), residues: 1068
  helix:  2.23 (0.28), residues: 359
  sheet: -0.37 (0.31), residues: 255
  loop : -0.78 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 197 
 TYR   0.015   0.001   TYR A 303 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.025   0.002   TRP B  63 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8708)
  covalent geometry    : angle       0.59752 (11809)
  SS BOND              : bond        0.00185 (    4)
  SS BOND              : angle       1.89408 (    8)
  hydrogen bonds       : bond        0.03271 (  430)
  hydrogen bonds       : angle       4.41685 ( 1209)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9044 (ptp-110) cc_final: 0.8711 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9217 (tppt) cc_final: 0.8972 (tppt)
REVERT: B   89 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8107 (ptpp)
REVERT: B  118 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (m-30)
REVERT: B  214 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7765 (mpp80)
REVERT: G   18 GLN cc_start: 0.8671 (tp-100) cc_final: 0.8428 (tp-100)
REVERT: G   21 MET cc_start: 0.9395 (tpp) cc_final: 0.9073 (ttp)
REVERT: G   41 CYS cc_start: 0.7357 (t) cc_final: 0.7022 (t)
REVERT: G   47 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: R   78 MET cc_start: 0.7578 (mtp) cc_final: 0.7365 (ttt)
REVERT: R   79 LYS cc_start: 0.8147 (tttt) cc_final: 0.7646 (mmmt)
REVERT: R   92 GLN cc_start: 0.8250 (tp40) cc_final: 0.7502 (tp-100)
REVERT: R  226 LYS cc_start: 0.6349 (tppt) cc_final: 0.6081 (mmtm)
REVERT: R  275 LYS cc_start: 0.7501 (tttt) cc_final: 0.7260 (tttt)
  outliers start: 21
  outliers final: 14
  residues processed: 175
  average time/residue: 0.1111
  time to fit residues: 25.6121
Evaluate side-chains
  169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  288 TRP
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  323 CYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 56 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.123246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.087691 restraints weight = 17139.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 3.21
r_work: 0.3340 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8713  Z= 0.124
  Angle     :  0.618  10.803  11817  Z= 0.318
  Chirality :  0.043   0.341   1351
  Planarity :  0.004   0.046   1486
  Dihedral  :  4.172  25.430   1169
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.88 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.27), residues: 1068
  helix:  2.20 (0.28), residues: 359
  sheet: -0.40 (0.30), residues: 271
  loop : -0.76 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 197 
 TYR   0.020   0.001   TYR A 303 
 PHE   0.017   0.001   PHE B 292 
 TRP   0.029   0.002   TRP B  63 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8708)
  covalent geometry    : angle       0.61699 (11809)
  SS BOND              : bond        0.00164 (    4)
  SS BOND              : angle       1.31334 (    8)
  hydrogen bonds       : bond        0.03247 (  430)
  hydrogen bonds       : angle       4.40573 ( 1209)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9033 (ptp-110) cc_final: 0.8697 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9201 (tppt) cc_final: 0.8959 (tppt)
REVERT: B   89 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8120 (ptpp)
REVERT: B  118 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8084 (m-30)
REVERT: B  214 ARG cc_start: 0.7990 (mpp80) cc_final: 0.7745 (mpp80)
REVERT: G   18 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8442 (tp-100)
REVERT: G   20 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8563 (pttm)
REVERT: G   21 MET cc_start: 0.9374 (tpp) cc_final: 0.9045 (ttp)
REVERT: G   47 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: R   78 MET cc_start: 0.7581 (mtp) cc_final: 0.7379 (ttt)
REVERT: R   79 LYS cc_start: 0.8159 (tttt) cc_final: 0.7666 (mmmt)
REVERT: R  226 LYS cc_start: 0.6384 (tppt) cc_final: 0.6101 (mmtm)
REVERT: R  275 LYS cc_start: 0.7529 (tttt) cc_final: 0.7265 (tttt)
  outliers start: 23
  outliers final: 17
  residues processed: 180
  average time/residue: 0.1036
  time to fit residues: 24.6061
Evaluate side-chains
  180 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  288 TRP
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.119860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.084374 restraints weight = 17306.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.17
r_work: 0.3244 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8713  Z= 0.213
  Angle     :  0.682   9.526  11817  Z= 0.351
  Chirality :  0.045   0.346   1351
  Planarity :  0.004   0.048   1486
  Dihedral  :  4.500  24.930   1169
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.28 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.27), residues: 1068
  helix:  2.18 (0.28), residues: 358
  sheet: -0.61 (0.30), residues: 282
  loop : -0.80 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 197 
 TYR   0.022   0.002   TYR S  50 
 PHE   0.027   0.002   PHE B 292 
 TRP   0.031   0.002   TRP S  47 
 HIS   0.006   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8708)
  covalent geometry    : angle       0.68142 (11809)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       1.52273 (    8)
  hydrogen bonds       : bond        0.03520 (  430)
  hydrogen bonds       : angle       4.50915 ( 1209)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9101 (ptp-110) cc_final: 0.8731 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9241 (tppt) cc_final: 0.8998 (tppt)
REVERT: B   89 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8166 (ptpp)
REVERT: B  118 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8156 (m-30)
REVERT: B  214 ARG cc_start: 0.7989 (mpp80) cc_final: 0.7745 (mpp80)
REVERT: G   18 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8568 (tp-100)
REVERT: G   20 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8499 (pttm)
REVERT: G   21 MET cc_start: 0.9361 (tpp) cc_final: 0.9075 (ttp)
REVERT: G   47 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: R   78 MET cc_start: 0.7591 (mtp) cc_final: 0.7356 (ttt)
REVERT: R   79 LYS cc_start: 0.8180 (tttt) cc_final: 0.7685 (mmmt)
REVERT: R  226 LYS cc_start: 0.6364 (tppt) cc_final: 0.6105 (mmtm)
REVERT: R  275 LYS cc_start: 0.7523 (tttt) cc_final: 0.7251 (tttt)
REVERT: R  323 CYS cc_start: 0.9530 (t) cc_final: 0.9181 (p)
  outliers start: 21
  outliers final: 15
  residues processed: 167
  average time/residue: 0.1114
  time to fit residues: 24.2311
Evaluate side-chains
  169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  288 TRP
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** R  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.121758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.086165 restraints weight = 17256.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.19
r_work: 0.3277 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8713  Z= 0.146
  Angle     :  0.672  13.086  11817  Z= 0.338
  Chirality :  0.044   0.317   1351
  Planarity :  0.004   0.053   1486
  Dihedral  :  4.429  26.664   1169
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.60 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.27), residues: 1068
  helix:  2.07 (0.28), residues: 358
  sheet: -0.66 (0.30), residues: 282
  loop : -0.77 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 197 
 TYR   0.015   0.001   TYR A 303 
 PHE   0.025   0.001   PHE S  68 
 TRP   0.029   0.002   TRP B  63 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8708)
  covalent geometry    : angle       0.67171 (11809)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       1.13379 (    8)
  hydrogen bonds       : bond        0.03392 (  430)
  hydrogen bonds       : angle       4.53945 ( 1209)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 ARG cc_start: 0.9096 (ptp-110) cc_final: 0.8760 (ptp-110)
REVERT: B   23 LYS cc_start: 0.9219 (tppt) cc_final: 0.8975 (tppt)
REVERT: B   89 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8101 (ptpp)
REVERT: B  118 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (m-30)
REVERT: B  214 ARG cc_start: 0.8005 (mpp80) cc_final: 0.7763 (mpp80)
REVERT: G   18 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8479 (tp-100)
REVERT: G   20 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8536 (pttm)
REVERT: G   21 MET cc_start: 0.9377 (tpp) cc_final: 0.9073 (ttp)
REVERT: G   47 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: R   79 LYS cc_start: 0.8150 (tttt) cc_final: 0.7654 (mmmt)
REVERT: R  226 LYS cc_start: 0.6320 (tppt) cc_final: 0.6065 (mmtm)
REVERT: R  275 LYS cc_start: 0.7489 (tttt) cc_final: 0.7223 (tttt)
REVERT: R  323 CYS cc_start: 0.9517 (t) cc_final: 0.9212 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 168
  average time/residue: 0.1112
  time to fit residues: 24.3847
Evaluate side-chains
  169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  345 GLN
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   80 HIS
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  288 TRP
Chi-restraints excluded: chain S residue   68 PHE
Chi-restraints excluded: chain S residue   76 LYS
Chi-restraints excluded: chain S residue  157 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** R  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 321 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.122351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.086749 restraints weight = 17295.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.21
r_work: 0.3289 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8713  Z= 0.143
  Angle     :  0.662  11.166  11817  Z= 0.336
  Chirality :  0.043   0.291   1351
  Planarity :  0.004   0.051   1486
  Dihedral  :  4.355  26.896   1169
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 21.25 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.27), residues: 1068
  helix:  2.12 (0.28), residues: 357
  sheet: -0.62 (0.30), residues: 282
  loop : -0.80 (0.32), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 197 
 TYR   0.014   0.001   TYR A 297 
 PHE   0.022   0.001   PHE S  68 
 TRP   0.026   0.002   TRP S  47 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8708)
  covalent geometry    : angle       0.66157 (11809)
  SS BOND              : bond        0.00182 (    4)
  SS BOND              : angle       1.03994 (    8)
  hydrogen bonds       : bond        0.03343 (  430)
  hydrogen bonds       : angle       4.43345 ( 1209)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2815.47 seconds
wall clock time: 48 minutes 50.51 seconds (2930.51 seconds total)