Starting phenix.real_space_refine
on Fri Aug 22 21:31:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f53_31456/08_2025/7f53_31456.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      63      5.16       5
     C    5165      2.51       5
     N    1407      2.21       5
     O    1517      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8153
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1885
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    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: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2133
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 7, 'TRANS': 265}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 133
      Number of conformers: 3
      Conformer: "A"
        Number of residues, atoms: 13, 114
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
      Conformer: "C"
        Number of residues, atoms: 12, 104
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 98
      Conformer: "B"
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 98
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AGLU L   5 " occ=0.45
      ... (16 atoms not shown)
      pdb=" OE2CGLU L   5 " occ=0.55
    residue:
      pdb=" N  AHIS L   6 " occ=0.20
      ... (18 atoms not shown)
      pdb=" NE2BHIS L   6 " occ=0.80
  Time building chain proxies: 1.84, per 1000 atoms: 0.23
  Number of scatterers: 8153
  At special positions: 0
  Unit cell: (86.19, 95.316, 123.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      63     16.00
     O    1517      8.00
     N    1407      7.00
     C    5165      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.05
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  40 " - pdb=" SG  CYS R 279 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 271 " - pdb=" SG  CYS R 277 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 384.9 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      43.3% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.593A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.997A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.727A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.668A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.459A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.921A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.526A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 47 through 72
      removed outlier: 3.809A  pdb=" N   PHE R  51 " --> pdb=" O   SER R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 110
    Processing helix  chain 'R' and resid 117 through 153
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 162 through 187
    Processing helix  chain 'R' and resid 192 through 228
      removed outlier: 3.749A  pdb=" N   VAL R 228 " --> pdb=" O   LYS R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 271
      removed outlier: 3.802A  pdb=" N   PHE R 254 " --> pdb=" O   LEU R 250 " (cutoff:3.500A)
      Proline residue:  R 260  - end of helix
    Processing helix  chain 'R' and resid 274 through 282
      removed outlier: 3.603A  pdb=" N   CYS R 279 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 283 through 298
      removed outlier: 3.772A  pdb=" N   ILE R 289 " --> pdb=" O   ASN R 285 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 301
      No H-bonds generated for 'chain 'R' and resid 299 through 301'
    Processing helix  chain 'R' and resid 302 through 305
      removed outlier: 3.565A  pdb=" N   ARG R 305 " --> pdb=" O   TYR R 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 302 through 305'
    Processing helix  chain 'R' and resid 306 through 320
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.332A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.308A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.804A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.582A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.155A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.565A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.803A  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: 3.668A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.680A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.610A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.635A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.687A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    452 hydrogen bonds defined for protein.
    1281 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: 1.25

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2141
        1.33 -     1.45: 1814
        1.45 -     1.58: 4261
        1.58 -     1.70: 0
        1.70 -     1.83: 89
  Bond restraints: 8305
  Sorted by residual:
  bond pdb=" C   VAL A 287 "
       pdb=" O   VAL A 287 "
    ideal  model  delta    sigma   weight residual
    1.238  1.207  0.031 1.10e-02 8.26e+03 7.79e+00
  bond pdb=" CB  ASP B  76 "
       pdb=" CG  ASP B  76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.464  0.052 2.50e-02 1.60e+03 4.30e+00
  bond pdb=" C   VAL B 327 "
       pdb=" O   VAL B 327 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.021 1.07e-02 8.73e+03 3.72e+00
  bond pdb=" CG  LEU B 318 "
       pdb=" CD2 LEU B 318 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.82e+00
  bond pdb=" CA  ASN R  72 "
       pdb=" C   ASN R  72 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 1.26e-02 6.30e+03 2.82e+00
  ... (remaining 8300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 10561
        1.76 -     3.52: 579
        3.52 -     5.28: 79
        5.28 -     7.04: 14
        7.04 -     8.80: 7
  Bond angle restraints: 11240
  Sorted by residual:
  angle pdb=" N   ASN R  72 "
        pdb=" CA  ASN R  72 "
        pdb=" C   ASN R  72 "
      ideal   model   delta    sigma   weight residual
     108.67  115.27   -6.60 1.55e+00 4.16e-01 1.81e+01
  angle pdb=" N   VAL A 287 "
        pdb=" CA  VAL A 287 "
        pdb=" C   VAL A 287 "
      ideal   model   delta    sigma   weight residual
     107.75  113.84   -6.09 1.46e+00 4.69e-01 1.74e+01
  angle pdb=" N   ASN R 294 "
        pdb=" CA  ASN R 294 "
        pdb=" C   ASN R 294 "
      ideal   model   delta    sigma   weight residual
     111.36  106.92    4.44 1.09e+00 8.42e-01 1.66e+01
  angle pdb=" N   TYR R 157 "
        pdb=" CA  TYR R 157 "
        pdb=" C   TYR R 157 "
      ideal   model   delta    sigma   weight residual
     110.80  119.22   -8.42 2.13e+00 2.20e-01 1.56e+01
  angle pdb=" N   ALA B 326 "
        pdb=" CA  ALA B 326 "
        pdb=" C   ALA B 326 "
      ideal   model   delta    sigma   weight residual
     109.07  114.60   -5.53 1.52e+00 4.33e-01 1.32e+01
  ... (remaining 11235 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.94: 4840
       27.94 -    55.89: 112
       55.89 -    83.83: 14
       83.83 -   111.78: 2
      111.78 -   139.72: 1
  Dihedral angle restraints: 4969
    sinusoidal: 1954
      harmonic: 3015
  Sorted by residual:
  dihedral pdb=" CB  CYS R  40 "
           pdb=" SG  CYS R  40 "
           pdb=" SG  CYS R 279 "
           pdb=" CB  CYS R 279 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -42.91  -43.09     1      1.00e+01 1.00e-02 2.59e+01
  dihedral pdb=" CB CGLU L   5 "
           pdb=" CG CGLU L   5 "
           pdb=" CD CGLU L   5 "
           pdb=" OE1CGLU L   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  139.72 -139.72     1      3.00e+01 1.11e-03 1.88e+01
  dihedral pdb=" CA  TRP R 258 "
           pdb=" C   TRP R 258 "
           pdb=" N   ALA R 259 "
           pdb=" CA  ALA R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.93  -18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 4966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 906
       0.057 -    0.115: 310
       0.115 -    0.172: 57
       0.172 -    0.229: 4
       0.229 -    0.287: 5
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" CA  TYR R 157 "
            pdb=" N   TYR R 157 "
            pdb=" C   TYR R 157 "
            pdb=" CB  TYR R 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.05e+00
  chirality pdb=" CA  ASN R  72 "
            pdb=" N   ASN R  72 "
            pdb=" C   ASN R  72 "
            pdb=" CB  ASN R  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  HIS R 158 "
            pdb=" N   HIS R 158 "
            pdb=" C   HIS R 158 "
            pdb=" CB  HIS R 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1279 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 382 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ILE A 382 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ILE A 382 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ILE A 383 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G  17 "    0.015 2.00e-02 2.50e+03   3.00e-02 8.98e+00
        pdb=" C   GLU G  17 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLU G  17 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN G  18 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 381 "   -0.015 2.00e-02 2.50e+03   2.93e-02 8.56e+00
        pdb=" C   ASP A 381 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP A 381 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A 382 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1538
        2.76 -     3.30: 7675
        3.30 -     3.83: 13217
        3.83 -     4.37: 16354
        4.37 -     4.90: 28407
  Nonbonded interactions: 67191
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OG  SER R 116 "
            pdb=" N   PHE R 117 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" ND2 ASN A 278 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OD2 ASP R 122 "
            pdb=" OH  TYR L   2 "
     model   vdw
     2.261 3.040
  ... (remaining 67186 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=0.20 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.310
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
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      :  0.008   0.062   8309  Z= 0.353
  Angle     :  0.920   8.799  11248  Z= 0.537
  Chirality :  0.058   0.287   1282
  Planarity :  0.006   0.032   1428
  Dihedral  : 12.117 139.723   3003
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.08 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  3.02 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.25), residues: 1014
  helix:  1.16 (0.23), residues: 405
  sheet:  0.93 (0.34), residues: 225
  loop :  0.39 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.002   ARG N  98 
 TYR   0.029   0.003   TYR A 339 
 PHE   0.050   0.004   PHE N 108 
 TRP   0.027   0.004   TRP B  99 
 HIS   0.014   0.003   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00804 ( 8305)
  covalent geometry    : angle       0.91870 (11240)
  SS BOND              : bond        0.00924 (    4)
  SS BOND              : angle       2.20671 (    8)
  hydrogen bonds       : bond        0.15718 (  452)
  hydrogen bonds       : angle       6.69471 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 238
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  216 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6564 (tptp)
REVERT: A  222 PHE cc_start: 0.7425 (m-80) cc_final: 0.7158 (m-80)
REVERT: A  381 ASP cc_start: 0.7331 (m-30) cc_final: 0.6985 (m-30)
REVERT: B  201 SER cc_start: 0.8908 (t) cc_final: 0.8458 (p)
REVERT: B  280 LYS cc_start: 0.8659 (tttt) cc_final: 0.8365 (tttm)
REVERT: B  307 VAL cc_start: 0.8620 (m) cc_final: 0.8400 (t)
REVERT: N  111 THR cc_start: 0.8550 (p) cc_final: 0.7774 (p)
REVERT: R  183 LEU cc_start: 0.8659 (mm) cc_final: 0.8096 (tt)
REVERT: R  200 MET cc_start: 0.5299 (mtt) cc_final: 0.5008 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 241
  average time/residue: 0.4670
  time to fit residues: 119.7028
Evaluate side-chains
  149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   73 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 175 GLN
B 220 GLN
B 266 HIS
G  18 GLN
N 120 GLN
R  72 ASN
L   6 HIS    A

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.177764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130741 restraints weight = 22318.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 4.43
r_work: 0.3455 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8309  Z= 0.155
  Angle     :  0.582   7.357  11248  Z= 0.318
  Chirality :  0.043   0.223   1282
  Planarity :  0.004   0.041   1428
  Dihedral  :  4.947  50.949   1127
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.38 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 13.87 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1014
  helix:  2.32 (0.24), residues: 410
  sheet:  1.27 (0.34), residues: 220
  loop :  0.17 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  27 
 TYR   0.013   0.001   TYR B 289 
 PHE   0.017   0.002   PHE B 241 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8305)
  covalent geometry    : angle       0.58183 (11240)
  SS BOND              : bond        0.00252 (    4)
  SS BOND              : angle       0.60841 (    8)
  hydrogen bonds       : bond        0.05103 (  452)
  hydrogen bonds       : angle       4.51232 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 171
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6833 (mmm160)
REVERT: A  216 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7081 (tptp)
REVERT: A  314 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7805 (pm20)
REVERT: B   46 ARG cc_start: 0.8545 (ptm160) cc_final: 0.8090 (ptm160)
REVERT: B   59 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8616 (t80)
REVERT: B  201 SER cc_start: 0.9073 (t) cc_final: 0.8840 (p)
REVERT: B  217 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8256 (ptt)
REVERT: G   18 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6631 (tm130)
REVERT: G   38 MET cc_start: 0.8196 (ttt) cc_final: 0.7989 (ttm)
REVERT: G   62 ARG cc_start: 0.6785 (tpp80) cc_final: 0.6558 (tpp80)
REVERT: N  109 ASP cc_start: 0.8506 (p0) cc_final: 0.8250 (p0)
REVERT: R  316 ILE cc_start: 0.6066 (mt) cc_final: 0.5815 (mp)
REVERT: L   11 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8801 (mmpt)
  outliers start: 40
  outliers final: 15
  residues processed: 189
  average time/residue: 0.4552
  time to fit residues: 91.6187
Evaluate side-chains
  160 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   18 GLN
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   54 LEU
Chi-restraints excluded: chain R residue   73 LYS
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 68 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
B 176 GLN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.174864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.127811 restraints weight = 24592.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 4.45
r_work: 0.3408 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3403
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8309  Z= 0.153
  Angle     :  0.533   5.298  11248  Z= 0.295
  Chirality :  0.042   0.146   1282
  Planarity :  0.004   0.043   1428
  Dihedral  :  4.771  52.551   1127
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.98 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 15.32 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.26), residues: 1014
  helix:  2.43 (0.25), residues: 419
  sheet:  1.11 (0.33), residues: 224
  loop :  0.23 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  49 
 TYR   0.014   0.001   TYR N  60 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8305)
  covalent geometry    : angle       0.53291 (11240)
  SS BOND              : bond        0.00270 (    4)
  SS BOND              : angle       0.67396 (    8)
  hydrogen bonds       : bond        0.04763 (  452)
  hydrogen bonds       : angle       4.27963 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 151
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7640 (mm110) cc_final: 0.6947 (mt0)
REVERT: A  216 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7356 (tptp)
REVERT: A  283 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7118 (mmt90)
REVERT: A  370 GLU cc_start: 0.7057 (tp30) cc_final: 0.6823 (tp30)
REVERT: B   46 ARG cc_start: 0.8663 (ptm160) cc_final: 0.7594 (pmt170)
REVERT: B   59 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8513 (t80)
REVERT: B  217 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8201 (ptt)
REVERT: B  270 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8836 (pp)
REVERT: G   27 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7594 (mpt-90)
REVERT: G   38 MET cc_start: 0.8018 (ttt) cc_final: 0.7805 (ttm)
REVERT: N   89 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8195 (pt0)
REVERT: N  120 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7834 (mt0)
REVERT: R  189 ASP cc_start: 0.8804 (t0) cc_final: 0.8547 (t70)
REVERT: R  200 MET cc_start: 0.5372 (mtt) cc_final: 0.5171 (mtp)
REVERT: R  316 ILE cc_start: 0.6117 (mt) cc_final: 0.5852 (mp)
REVERT: L   11 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8740 (mmpt)
  outliers start: 46
  outliers final: 21
  residues processed: 175
  average time/residue: 0.4308
  time to fit residues: 80.5096
Evaluate side-chains
  173 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue   73 LYS
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0070
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
R 273 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.177642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.136150 restraints weight = 24186.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 5.31
r_work: 0.3418 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8309  Z= 0.116
  Angle     :  0.488   5.392  11248  Z= 0.269
  Chirality :  0.040   0.143   1282
  Planarity :  0.004   0.043   1428
  Dihedral  :  4.609  53.195   1127
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.09 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 16.55 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.26), residues: 1014
  helix:  2.68 (0.25), residues: 413
  sheet:  1.04 (0.33), residues: 224
  loop :  0.29 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  62 
 TYR   0.013   0.001   TYR N  60 
 PHE   0.023   0.001   PHE B 241 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8305)
  covalent geometry    : angle       0.48756 (11240)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       0.65002 (    8)
  hydrogen bonds       : bond        0.04147 (  452)
  hydrogen bonds       : angle       4.07554 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 157
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6669 (mmm160)
REVERT: A   31 GLN cc_start: 0.7588 (mm110) cc_final: 0.6943 (mt0)
REVERT: A  216 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7402 (tptp)
REVERT: A  314 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7864 (pm20)
REVERT: B   44 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7954 (pt0)
REVERT: B   46 ARG cc_start: 0.8698 (ptm160) cc_final: 0.8115 (ptm160)
REVERT: B   59 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8565 (t80)
REVERT: B  217 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8277 (ptt)
REVERT: B  228 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8352 (m-30)
REVERT: G   20 LYS cc_start: 0.7821 (pptt) cc_final: 0.7497 (ptpt)
REVERT: N   82 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7458 (tp40)
REVERT: N   89 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8282 (pt0)
REVERT: R  286 LEU cc_start: 0.7227 (tt) cc_final: 0.6807 (mp)
REVERT: R  309 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7436 (tt)
REVERT: L   11 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8741 (mmpt)
  outliers start: 42
  outliers final: 21
  residues processed: 180
  average time/residue: 0.4475
  time to fit residues: 85.7826
Evaluate side-chains
  166 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   73 LYS
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  269 ILE
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** N 120 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 = 0.4075 r_free = 0.4075 target = 0.171448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.130216 restraints weight = 19234.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 4.71
r_work: 0.3350 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8309  Z= 0.209
  Angle     :  0.575   6.209  11248  Z= 0.316
  Chirality :  0.044   0.162   1282
  Planarity :  0.004   0.044   1428
  Dihedral  :  4.907  53.324   1127
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 17.23 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1014
  helix:  2.38 (0.24), residues: 421
  sheet:  0.78 (0.33), residues: 230
  loop :  0.12 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  27 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.030   0.002   PHE N 108 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 8305)
  covalent geometry    : angle       0.57488 (11240)
  SS BOND              : bond        0.00334 (    4)
  SS BOND              : angle       0.90304 (    8)
  hydrogen bonds       : bond        0.05041 (  452)
  hydrogen bonds       : angle       4.36344 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 154
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.8485 (mt) cc_final: 0.8275 (mp)
REVERT: A  216 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7618 (tptp)
REVERT: A  283 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7224 (mmt90)
REVERT: A  370 GLU cc_start: 0.7171 (tp30) cc_final: 0.6909 (tp30)
REVERT: B   44 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7857 (pt0)
REVERT: B   46 ARG cc_start: 0.8706 (ptm160) cc_final: 0.7710 (pmt170)
REVERT: B   59 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8640 (t80)
REVERT: B  217 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8229 (ptt)
REVERT: G   20 LYS cc_start: 0.7929 (pptt) cc_final: 0.7584 (ptpt)
REVERT: G   27 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7713 (mpt-90)
REVERT: N    5 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7807 (mm-40)
REVERT: N   82 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7383 (tm-30)
REVERT: R  309 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (tt)
REVERT: L   11 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8718 (mmpt)
  outliers start: 51
  outliers final: 24
  residues processed: 186
  average time/residue: 0.4551
  time to fit residues: 90.0983
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue   73 LYS
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  203 THR
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain L residue    3 SER
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B 266 HIS
** N 120 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 = 0.4096 r_free = 0.4096 target = 0.173436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.129044 restraints weight = 13623.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.19
r_work: 0.3468 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8309  Z= 0.149
  Angle     :  0.518   5.853  11248  Z= 0.283
  Chirality :  0.042   0.140   1282
  Planarity :  0.004   0.045   1428
  Dihedral  :  4.751  54.168   1127
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 18.57 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.26), residues: 1014
  helix:  2.59 (0.24), residues: 414
  sheet:  0.88 (0.33), residues: 227
  loop :  0.12 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.027   0.002   PHE B 241 
 TRP   0.013   0.002   TRP B 169 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8305)
  covalent geometry    : angle       0.51768 (11240)
  SS BOND              : bond        0.00284 (    4)
  SS BOND              : angle       0.66666 (    8)
  hydrogen bonds       : bond        0.04473 (  452)
  hydrogen bonds       : angle       4.18749 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 139
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6661 (mmm160)
REVERT: A   31 GLN cc_start: 0.7490 (mm110) cc_final: 0.6959 (mt0)
REVERT: A  216 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7565 (tptp)
REVERT: A  283 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7143 (mmt90)
REVERT: B   44 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7824 (pt0)
REVERT: B   46 ARG cc_start: 0.8575 (ptm160) cc_final: 0.7652 (pmt170)
REVERT: B   59 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8591 (t80)
REVERT: B  105 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (t80)
REVERT: B  138 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7301 (mm-30)
REVERT: B  217 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8255 (ptt)
REVERT: G   20 LYS cc_start: 0.7909 (pptt) cc_final: 0.7558 (ptpt)
REVERT: G   27 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7549 (mpt-90)
REVERT: G   62 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6755 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7887 (mm-40)
REVERT: N   82 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7416 (tm-30)
REVERT: L   11 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (mmpt)
  outliers start: 43
  outliers final: 21
  residues processed: 164
  average time/residue: 0.4478
  time to fit residues: 77.9685
Evaluate side-chains
  163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  203 THR
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.0050
   chunk 93 optimal weight:    0.0870
   chunk 78 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0010
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.2376

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.178887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.137137 restraints weight = 19490.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 4.53
r_work: 0.3470 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3483 r_free = 0.3483    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.4493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8309  Z= 0.101
  Angle     :  0.478   5.915  11248  Z= 0.262
  Chirality :  0.040   0.139   1282
  Planarity :  0.004   0.042   1428
  Dihedral  :  4.169  54.721   1123
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.80 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.27), residues: 1014
  helix:  2.75 (0.25), residues: 415
  sheet:  1.06 (0.33), residues: 224
  loop :  0.18 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.009   0.001   PHE B 199 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.001   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 8305)
  covalent geometry    : angle       0.47819 (11240)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       0.52798 (    8)
  hydrogen bonds       : bond        0.03773 (  452)
  hydrogen bonds       : angle       4.01583 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 154
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6576 (mmm160)
REVERT: A   31 GLN cc_start: 0.7428 (mm110) cc_final: 0.6922 (mt0)
REVERT: A  216 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7438 (tptp)
REVERT: A  230 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7671 (mm-30)
REVERT: A  299 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6957 (mp0)
REVERT: B   46 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8035 (ptm160)
REVERT: B   59 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8553 (t80)
REVERT: B  217 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8289 (ptt)
REVERT: G   20 LYS cc_start: 0.7884 (pptt) cc_final: 0.7548 (ptpt)
REVERT: G   27 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7449 (mpt-90)
REVERT: G   62 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6740 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7871 (mm-40)
REVERT: N   82 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7304 (tm-30)
REVERT: R  286 LEU cc_start: 0.7014 (tt) cc_final: 0.6674 (mp)
REVERT: L   11 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8619 (mmpt)
  outliers start: 34
  outliers final: 11
  residues processed: 173
  average time/residue: 0.4183
  time to fit residues: 77.2110
Evaluate side-chains
  155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.176702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.130721 restraints weight = 15320.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 3.54
r_work: 0.3448 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3450
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8309  Z= 0.120
  Angle     :  0.500   7.283  11248  Z= 0.275
  Chirality :  0.041   0.139   1282
  Planarity :  0.004   0.039   1428
  Dihedral  :  4.186  54.685   1123
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.47 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.26), residues: 1014
  helix:  2.70 (0.25), residues: 415
  sheet:  0.90 (0.34), residues: 217
  loop :  0.25 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.016   0.001   PHE N 108 
 TRP   0.023   0.001   TRP R 258 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8305)
  covalent geometry    : angle       0.50015 (11240)
  SS BOND              : bond        0.00245 (    4)
  SS BOND              : angle       0.64851 (    8)
  hydrogen bonds       : bond        0.03977 (  452)
  hydrogen bonds       : angle       4.03518 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6564 (mmm160)
REVERT: A  216 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7435 (tptp)
REVERT: A  230 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7648 (mm-30)
REVERT: A  283 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7014 (mmt90)
REVERT: A  299 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6885 (mp0)
REVERT: B   46 ARG cc_start: 0.8600 (ptm160) cc_final: 0.7993 (ptm160)
REVERT: B   59 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8530 (t80)
REVERT: B  138 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7368 (mm-30)
REVERT: B  217 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8196 (ptt)
REVERT: G   20 LYS cc_start: 0.7871 (pptt) cc_final: 0.7513 (ptpt)
REVERT: G   62 ARG cc_start: 0.7119 (tpp80) cc_final: 0.6661 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7902 (mm-40)
REVERT: N   82 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7282 (tm-30)
REVERT: N   86 LEU cc_start: 0.8492 (mt) cc_final: 0.8189 (mm)
REVERT: R  286 LEU cc_start: 0.7007 (tt) cc_final: 0.6616 (mp)
REVERT: L   11 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8602 (mmpt)
  outliers start: 32
  outliers final: 16
  residues processed: 150
  average time/residue: 0.4416
  time to fit residues: 70.3755
Evaluate side-chains
  152 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  268 TYR
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.9700

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.176753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.131399 restraints weight = 17308.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 3.90
r_work: 0.3418 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8309  Z= 0.124
  Angle     :  0.505   7.869  11248  Z= 0.276
  Chirality :  0.041   0.138   1282
  Planarity :  0.004   0.036   1428
  Dihedral  :  4.191  54.860   1123
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.92 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.27), residues: 1014
  helix:  2.74 (0.25), residues: 413
  sheet:  0.74 (0.34), residues: 224
  loop :  0.18 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.015   0.001   PHE N 108 
 TRP   0.066   0.002   TRP R 258 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8305)
  covalent geometry    : angle       0.50502 (11240)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       0.59307 (    8)
  hydrogen bonds       : bond        0.04037 (  452)
  hydrogen bonds       : angle       4.07443 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6427 (mmm-85)
REVERT: A   31 GLN cc_start: 0.7370 (mm110) cc_final: 0.6843 (mt0)
REVERT: A  216 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7424 (tptp)
REVERT: A  230 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7624 (mm-30)
REVERT: A  283 ARG cc_start: 0.7392 (mtt180) cc_final: 0.6943 (mmt90)
REVERT: A  299 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6860 (mp0)
REVERT: B   46 ARG cc_start: 0.8576 (ptm160) cc_final: 0.7558 (pmt170)
REVERT: B   59 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8572 (t80)
REVERT: B  138 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7420 (mm-30)
REVERT: B  217 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8172 (ptt)
REVERT: G   20 LYS cc_start: 0.7754 (pptt) cc_final: 0.7385 (ptpt)
REVERT: G   62 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6698 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7854 (mm-40)
REVERT: N   82 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7225 (tm-30)
REVERT: N   86 LEU cc_start: 0.8362 (mt) cc_final: 0.8020 (mm)
REVERT: L   11 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8625 (mmpt)
  outliers start: 27
  outliers final: 16
  residues processed: 146
  average time/residue: 0.4469
  time to fit residues: 69.2203
Evaluate side-chains
  148 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.175528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.129822 restraints weight = 14069.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 3.37
r_work: 0.3436 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3441
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3441 r_free = 0.3441    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3441
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8309  Z= 0.142
  Angle     :  0.527  10.531  11248  Z= 0.286
  Chirality :  0.042   0.140   1282
  Planarity :  0.004   0.036   1428
  Dihedral  :  4.278  54.894   1123
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.37 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.26), residues: 1014
  helix:  2.66 (0.25), residues: 413
  sheet:  0.64 (0.34), residues: 225
  loop :  0.17 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  27 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.018   0.002   PHE N 108 
 TRP   0.048   0.002   TRP R 258 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8305)
  covalent geometry    : angle       0.52733 (11240)
  SS BOND              : bond        0.00236 (    4)
  SS BOND              : angle       0.64110 (    8)
  hydrogen bonds       : bond        0.04212 (  452)
  hydrogen bonds       : angle       4.11858 ( 1281)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 125
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6473 (mmm-85)
REVERT: A   31 GLN cc_start: 0.7379 (mm110) cc_final: 0.6822 (mt0)
REVERT: A   60 MET cc_start: 0.3072 (OUTLIER) cc_final: -0.0127 (tmm)
REVERT: A  216 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7427 (tptp)
REVERT: A  230 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7654 (mm-30)
REVERT: A  283 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6963 (mmt90)
REVERT: A  299 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6942 (mp0)
REVERT: B   46 ARG cc_start: 0.8558 (ptm160) cc_final: 0.7580 (pmt170)
REVERT: B   59 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8548 (t80)
REVERT: B  138 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7407 (mm-30)
REVERT: B  217 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8199 (ptt)
REVERT: G   20 LYS cc_start: 0.7804 (pptt) cc_final: 0.7445 (ptpt)
REVERT: G   62 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6720 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7874 (mm-40)
REVERT: N   82 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7289 (tm-30)
REVERT: N   86 LEU cc_start: 0.8424 (mt) cc_final: 0.8065 (mm)
REVERT: L   11 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8613 (mmpt)
  outliers start: 25
  outliers final: 16
  residues processed: 138
  average time/residue: 0.4808
  time to fit residues: 70.6311
Evaluate side-chains
  147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  282 SER
Chi-restraints excluded: chain R residue  289 ILE
Chi-restraints excluded: chain R residue  304 LEU
Chi-restraints excluded: chain R residue  309 LEU
Chi-restraints excluded: chain L residue   11 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.174711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130039 restraints weight = 12496.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 3.14
r_work: 0.3450 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3457 r_free = 0.3457    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8309  Z= 0.146
  Angle     :  0.535  11.088  11248  Z= 0.290
  Chirality :  0.042   0.139   1282
  Planarity :  0.004   0.034   1428
  Dihedral  :  4.336  55.193   1123
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.26 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1014
  helix:  2.62 (0.24), residues: 413
  sheet:  0.57 (0.34), residues: 225
  loop :  0.12 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G  27 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.020   0.002   PHE N 108 
 TRP   0.046   0.002   TRP R 258 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8305)
  covalent geometry    : angle       0.53521 (11240)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.65916 (    8)
  hydrogen bonds       : bond        0.04296 (  452)
  hydrogen bonds       : angle       4.16174 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2694.43 seconds
wall clock time: 46 minutes 34.05 seconds (2794.05 seconds total)