Starting phenix.real_space_refine
on Wed Mar 12 16:06:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f53_31456/03_2025/7f53_31456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f53_31456/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f53_31456/03_2025/7f53_31456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f53_31456/03_2025/7f53_31456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f53_31456/03_2025/7f53_31456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f53_31456/03_2025/7f53_31456.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.10, per 1000 atoms: 0.63
  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: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.91
  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: 2.18

  Time building geometry restraints manager: 2.37 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:             0.390
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.640
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.400
-------------------------------------------------------------------------------
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   8305  Z= 0.540
  Angle     :  0.919   8.799  11240  Z= 0.536
  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 : 8.32
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (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
 TRP   0.027   0.004   TRP B  99 
 HIS   0.014   0.003   HIS B 183 
 PHE   0.050   0.004   PHE N 108 
 TYR   0.029   0.003   TYR A 339 
 ARG   0.014   0.002   ARG N  98 

*********************** 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  : 0.835 
Fit side-chains
REVERT: A  216 LYS cc_start: 0.7230 (mmtt) cc_final: 0.6563 (tptp)
REVERT: A  222 PHE cc_start: 0.7425 (m-80) cc_final: 0.7184 (m-80)
REVERT: A  381 ASP cc_start: 0.7331 (m-30) cc_final: 0.6983 (m-30)
REVERT: B  105 TYR cc_start: 0.8288 (t80) cc_final: 0.8031 (t80)
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: 0.8364 (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: 0.7775 (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: 1.0894
  time to fit residues: 279.3824
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  : 0.823 
-------------------------------------------------------------------------------
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 84 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0870
   overall best weight:    0.6960

-------------------------------------------------------------------------------
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
R  76 HIS
L   6 HIS    A

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.180859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.139048 restraints weight = 20120.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 4.85
r_work: 0.3446 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    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 = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3455
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8305  Z= 0.180
  Angle     :  0.561   7.254  11240  Z= 0.306
  Chirality :  0.043   0.229   1282
  Planarity :  0.004   0.038   1428
  Dihedral  :  4.829  50.297   1127
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  0.99 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 13.65 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.26), residues: 1014
  helix:  2.37 (0.24), residues: 410
  sheet:  1.32 (0.34), residues: 220
  loop :  0.25 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.002   PHE B 241 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.007   0.001   ARG G  27 

*********************** 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
  213 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 175
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6816 (mmm160)
REVERT: A  216 LYS cc_start: 0.7845 (mmtt) cc_final: 0.6875 (tptp)
REVERT: A  314 GLU cc_start: 0.8783 (mm-30) cc_final: 0.7805 (pm20)
REVERT: B   46 ARG cc_start: 0.8436 (ptm160) cc_final: 0.7981 (ptm160)
REVERT: B   59 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (t80)
REVERT: B  105 TYR cc_start: 0.8708 (t80) cc_final: 0.8483 (t80)
REVERT: B  217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8248 (ptt)
REVERT: B  221 THR cc_start: 0.7842 (m) cc_final: 0.7613 (m)
REVERT: G   18 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6706 (tm130)
REVERT: G   22 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6543 (mt-10)
REVERT: G   38 MET cc_start: 0.8207 (ttt) cc_final: 0.7996 (ttm)
REVERT: G   62 ARG cc_start: 0.6733 (tpp80) cc_final: 0.6454 (tpp80)
REVERT: N  109 ASP cc_start: 0.8510 (p0) cc_final: 0.8247 (p0)
REVERT: R  316 ILE cc_start: 0.6060 (mt) cc_final: 0.5815 (mp)
REVERT: L   11 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8777 (mmpt)
  outliers start: 38
  outliers final: 15
  residues processed: 191
  average time/residue: 1.1888
  time to fit residues: 242.1747
Evaluate side-chains
  159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   21 SER
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 49 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
N  31 ASN
N 120 GLN
R 222 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.179473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.136604 restraints weight = 12661.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 3.19
r_work: 0.3539 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8305  Z= 0.171
  Angle     :  0.506   5.143  11240  Z= 0.278
  Chirality :  0.041   0.144   1282
  Planarity :  0.004   0.040   1428
  Dihedral  :  4.587  51.670   1127
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 16.55 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.26), residues: 1014
  helix:  2.65 (0.25), residues: 412
  sheet:  1.25 (0.34), residues: 215
  loop :  0.24 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.015   0.001   TYR N  60 
 ARG   0.009   0.000   ARG G  27 

*********************** 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
  199 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 162
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6715 (mmm160)
REVERT: A  216 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7160 (tptp)
REVERT: A  314 GLU cc_start: 0.8812 (mm-30) cc_final: 0.7992 (pm20)
REVERT: B   46 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7938 (ptm160)
REVERT: B   59 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8506 (t80)
REVERT: B  105 TYR cc_start: 0.8717 (t80) cc_final: 0.8381 (t80)
REVERT: B  270 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8856 (pp)
REVERT: G   18 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6823 (tm130)
REVERT: G   20 LYS cc_start: 0.7944 (pptt) cc_final: 0.7609 (ptpp)
REVERT: G   38 MET cc_start: 0.8222 (ttt) cc_final: 0.7984 (ttm)
REVERT: N   82 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7388 (tp40)
REVERT: N  120 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7751 (mt0)
REVERT: R  189 ASP cc_start: 0.8751 (t0) cc_final: 0.8521 (t70)
REVERT: R  286 LEU cc_start: 0.7179 (tt) cc_final: 0.6778 (mp)
REVERT: R  309 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7333 (tt)
REVERT: R  316 ILE cc_start: 0.6182 (mt) cc_final: 0.5915 (mp)
REVERT: L   11 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8731 (mmpt)
  outliers start: 37
  outliers final: 15
  residues processed: 179
  average time/residue: 0.9681
  time to fit residues: 186.0236
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
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  325 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   76 ASP
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   18 GLN
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 N residue  120 GLN
Chi-restraints excluded: chain R residue  173 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0270
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    1.1640

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
R 273 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.177011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.135604 restraints weight = 23479.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 5.26
r_work: 0.3403 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    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 = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8305  Z= 0.206
  Angle     :  0.511   5.475  11240  Z= 0.281
  Chirality :  0.041   0.142   1282
  Planarity :  0.004   0.037   1428
  Dihedral  :  4.329  52.640   1123
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.38 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 16.67 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.26), residues: 1014
  helix:  2.60 (0.25), residues: 419
  sheet:  1.06 (0.33), residues: 219
  loop :  0.29 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.021   0.002   PHE R 280 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.008   0.000   ARG G  27 

*********************** 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
  190 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6759 (mmm160)
REVERT: A  216 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7246 (tptp)
REVERT: B   44 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7813 (pt0)
REVERT: B   46 ARG cc_start: 0.8647 (ptm160) cc_final: 0.7665 (pmt170)
REVERT: B   59 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8587 (t80)
REVERT: B  301 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8148 (mmmt)
REVERT: G   18 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6958 (tm-30)
REVERT: G   20 LYS cc_start: 0.7832 (pptt) cc_final: 0.7470 (ptpt)
REVERT: N   82 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7299 (tp40)
REVERT: R  309 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7389 (tt)
REVERT: R  316 ILE cc_start: 0.6186 (mt) cc_final: 0.5889 (mp)
REVERT: L   11 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8714 (mmpt)
  outliers start: 44
  outliers final: 16
  residues processed: 173
  average time/residue: 1.0197
  time to fit residues: 189.1534
Evaluate side-chains
  162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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  325 THR
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   65 THR
Chi-restraints excluded: chain B residue  228 ASP
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   93 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  220 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.4108 r_free = 0.4108 target = 0.174758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128950 restraints weight = 15724.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.47
r_work: 0.3454 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8305  Z= 0.233
  Angle     :  0.525   6.419  11240  Z= 0.287
  Chirality :  0.042   0.142   1282
  Planarity :  0.004   0.036   1428
  Dihedral  :  4.396  53.529   1123
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.26), residues: 1014
  helix:  2.66 (0.24), residues: 415
  sheet:  0.98 (0.34), residues: 216
  loop :  0.20 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.022   0.002   PHE N 108 
 TYR   0.012   0.001   TYR A 339 
 ARG   0.009   0.000   ARG G  27 

*********************** 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
  185 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6645 (mmm160)
REVERT: A   31 GLN cc_start: 0.7552 (mm110) cc_final: 0.6965 (mt0)
REVERT: A  216 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7431 (tptp)
REVERT: A  283 ARG cc_start: 0.7467 (mtt180) cc_final: 0.7090 (mmt90)
REVERT: B   44 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7664 (pt0)
REVERT: B   46 ARG cc_start: 0.8567 (ptm160) cc_final: 0.7638 (pmt170)
REVERT: B   59 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8560 (t80)
REVERT: B  217 MET cc_start: 0.8268 (ptt) cc_final: 0.7963 (pmm)
REVERT: G   18 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6739 (tm130)
REVERT: G   20 LYS cc_start: 0.7926 (pptt) cc_final: 0.7570 (ptpt)
REVERT: G   27 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7817 (mpt-90)
REVERT: R  225 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7429 (ttp-170)
REVERT: R  309 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7482 (tt)
REVERT: R  316 ILE cc_start: 0.6387 (mt) cc_final: 0.6176 (mt)
REVERT: L   11 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8683 (mmpt)
  outliers start: 41
  outliers final: 18
  residues processed: 166
  average time/residue: 1.0785
  time to fit residues: 191.1738
Evaluate side-chains
  157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
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   65 THR
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   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  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  241 MET
Chi-restraints excluded: chain R residue  269 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.174337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.134291 restraints weight = 26003.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 5.92
r_work: 0.3348 rms_B_bonded: 5.30 restraints_weight: 2.0000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    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 = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3353
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8305  Z= 0.225
  Angle     :  0.513   6.002  11240  Z= 0.282
  Chirality :  0.042   0.141   1282
  Planarity :  0.004   0.035   1428
  Dihedral  :  4.352  53.978   1123
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.26), residues: 1014
  helix:  2.64 (0.24), residues: 415
  sheet:  0.95 (0.34), residues: 221
  loop :  0.19 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 211 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.012   0.001   TYR N 117 
 ARG   0.008   0.000   ARG G  27 

*********************** 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
  183 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6684 (mmm160)
REVERT: A   31 GLN cc_start: 0.7649 (mm110) cc_final: 0.7057 (mt0)
REVERT: A  216 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7509 (tptp)
REVERT: A  230 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7803 (mm-30)
REVERT: A  283 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7289 (mmt90)
REVERT: A  299 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6869 (mp0)
REVERT: B   44 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7876 (pt0)
REVERT: B   46 ARG cc_start: 0.8705 (ptm160) cc_final: 0.7713 (pmt170)
REVERT: B   59 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8641 (t80)
REVERT: B  138 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7413 (mm-30)
REVERT: B  217 MET cc_start: 0.8317 (ptt) cc_final: 0.8039 (pmm)
REVERT: G   18 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6541 (tm130)
REVERT: G   20 LYS cc_start: 0.7914 (pptt) cc_final: 0.7557 (ptpt)
REVERT: G   27 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7503 (mpt-90)
REVERT: N    5 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7792 (mm-40)
REVERT: R  309 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7449 (tt)
REVERT: R  316 ILE cc_start: 0.6224 (mt) cc_final: 0.6005 (mt)
REVERT: L   11 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8685 (mmpt)
  outliers start: 41
  outliers final: 22
  residues processed: 167
  average time/residue: 1.0925
  time to fit residues: 194.4704
Evaluate side-chains
  165 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
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  239 ASN
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 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   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  172 GLU
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   93 VAL
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   92 LEU
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  220 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 61 optimal weight:   10.0000
   chunk 92 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.171821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126439 restraints weight = 16091.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 3.47
r_work: 0.3422 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3424
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8305  Z= 0.301
  Angle     :  0.545   5.861  11240  Z= 0.300
  Chirality :  0.043   0.141   1282
  Planarity :  0.004   0.035   1428
  Dihedral  :  4.473  53.891   1123
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 18.57 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.26), residues: 1014
  helix:  2.54 (0.24), residues: 413
  sheet:  0.61 (0.33), residues: 232
  loop :  0.17 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.004   0.001   HIS G  44 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.007   0.001   ARG G  27 

*********************** 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
  177 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6674 (mmm160)
REVERT: A  230 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7682 (mm-30)
REVERT: A  283 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7138 (mmt90)
REVERT: A  299 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7003 (mp0)
REVERT: A  370 GLU cc_start: 0.7035 (tp30) cc_final: 0.6800 (tp30)
REVERT: B   44 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7845 (pt0)
REVERT: B   46 ARG cc_start: 0.8557 (ptm160) cc_final: 0.7619 (pmt170)
REVERT: B   59 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8614 (t80)
REVERT: B  111 TYR cc_start: 0.8729 (m-80) cc_final: 0.8516 (m-80)
REVERT: B  138 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: B  217 MET cc_start: 0.8275 (ptt) cc_final: 0.8008 (pmm)
REVERT: G   18 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6641 (tm130)
REVERT: G   20 LYS cc_start: 0.7902 (pptt) cc_final: 0.7536 (ptpt)
REVERT: G   27 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7549 (mpt-90)
REVERT: G   62 ARG cc_start: 0.7180 (tpp80) cc_final: 0.6692 (tpm-80)
REVERT: R  316 ILE cc_start: 0.6401 (mt) cc_final: 0.6188 (mp)
REVERT: L   11 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8723 (mmpt)
  outliers start: 41
  outliers final: 22
  residues processed: 164
  average time/residue: 1.0985
  time to fit residues: 192.2119
Evaluate side-chains
  155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  239 ASN
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 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   65 THR
Chi-restraints excluded: chain B residue  172 GLU
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  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  169 ILE
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  224 LYS
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  256 VAL
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 L residue   11 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0870
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.176543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.130427 restraints weight = 19507.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 4.24
r_work: 0.3403 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    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 = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8305  Z= 0.163
  Angle     :  0.502   6.063  11240  Z= 0.275
  Chirality :  0.041   0.141   1282
  Planarity :  0.004   0.035   1428
  Dihedral  :  4.261  54.724   1123
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 19.46 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.26), residues: 1014
  helix:  2.78 (0.24), residues: 413
  sheet:  0.77 (0.33), residues: 228
  loop :  0.18 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.031   0.001   PHE B 241 
 TYR   0.013   0.001   TYR N 117 
 ARG   0.006   0.000   ARG G  27 

*********************** 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
  171 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6552 (mmm160)
REVERT: A   31 GLN cc_start: 0.7360 (mm110) cc_final: 0.6823 (mt0)
REVERT: A  216 LYS cc_start: 0.8278 (mptt) cc_final: 0.7454 (tptp)
REVERT: A  230 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7697 (mm-30)
REVERT: A  299 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6912 (mp0)
REVERT: A  370 GLU cc_start: 0.7077 (tp30) cc_final: 0.6862 (tp30)
REVERT: B   46 ARG cc_start: 0.8619 (ptm160) cc_final: 0.7637 (pmt170)
REVERT: B   59 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8604 (t80)
REVERT: B  138 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: B  217 MET cc_start: 0.8183 (ptt) cc_final: 0.7913 (pmm)
REVERT: G   18 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6424 (tm130)
REVERT: G   20 LYS cc_start: 0.7859 (pptt) cc_final: 0.7512 (ptpt)
REVERT: G   27 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7372 (mpt-90)
REVERT: G   62 ARG cc_start: 0.7052 (tpp80) cc_final: 0.6575 (tpm-80)
REVERT: N    5 GLN cc_start: 0.8131 (mt0) cc_final: 0.7780 (mm-40)
REVERT: N  109 ASP cc_start: 0.8481 (p0) cc_final: 0.8274 (p0)
REVERT: L   11 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8728 (mmpt)
  outliers start: 38
  outliers final: 17
  residues processed: 154
  average time/residue: 1.0419
  time to fit residues: 172.0032
Evaluate side-chains
  153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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 B residue   37 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  223 THR
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  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 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 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:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4092 r_free = 0.4092 target = 0.174586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.127929 restraints weight = 23699.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 4.77
r_work: 0.3366 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.4549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8305  Z= 0.220
  Angle     :  0.524   6.293  11240  Z= 0.287
  Chirality :  0.041   0.141   1282
  Planarity :  0.004   0.034   1428
  Dihedral  :  4.302  54.635   1123
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.59 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.26), residues: 1014
  helix:  2.71 (0.24), residues: 413
  sheet:  0.60 (0.33), residues: 232
  loop :  0.16 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 258 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.018   0.002   PHE N 108 
 TYR   0.011   0.001   TYR N 117 
 ARG   0.006   0.000   ARG G  27 

*********************** 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
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   20 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6581 (mmm160)
REVERT: A   31 GLN cc_start: 0.7422 (mm110) cc_final: 0.6884 (mt0)
REVERT: A  283 ARG cc_start: 0.7472 (mtt180) cc_final: 0.7015 (mmt90)
REVERT: A  299 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6902 (mp0)
REVERT: A  370 GLU cc_start: 0.7126 (tp30) cc_final: 0.6873 (tp30)
REVERT: B   44 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7867 (pt0)
REVERT: B   46 ARG cc_start: 0.8617 (ptm160) cc_final: 0.7633 (pmt170)
REVERT: B   59 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8587 (t80)
REVERT: B  138 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7462 (mm-30)
REVERT: B  217 MET cc_start: 0.8257 (ptt) cc_final: 0.7969 (pmm)
REVERT: G   18 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6405 (tm130)
REVERT: G   20 LYS cc_start: 0.7838 (pptt) cc_final: 0.7485 (ptpt)
REVERT: G   62 ARG cc_start: 0.7128 (tpp80) cc_final: 0.6633 (tpm-80)
REVERT: N   86 LEU cc_start: 0.8455 (mt) cc_final: 0.8100 (mm)
REVERT: L   11 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8704 (mmpt)
  outliers start: 28
  outliers final: 18
  residues processed: 144
  average time/residue: 1.1421
  time to fit residues: 175.1461
Evaluate side-chains
  151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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  299 GLU
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   65 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  260 GLU
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  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  220 ARG
Chi-restraints excluded: chain R residue  245 ILE
Chi-restraints excluded: chain R residue  269 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0060
   chunk 56 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.176929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131904 restraints weight = 17212.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 3.60
r_work: 0.3437 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3439 r_free = 0.3439    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.4659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8305  Z= 0.160
  Angle     :  0.495   6.142  11240  Z= 0.273
  Chirality :  0.041   0.140   1282
  Planarity :  0.004   0.040   1428
  Dihedral  :  4.200  55.266   1123
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.27), residues: 1014
  helix:  2.76 (0.24), residues: 413
  sheet:  0.67 (0.33), residues: 235
  loop :  0.13 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 258 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.012   0.001   PHE A 376 
 TYR   0.010   0.001   TYR N 117 
 ARG   0.011   0.000   ARG G  27 

********************** 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
  158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7375 (mm110) cc_final: 0.6859 (mt0)
REVERT: A   60 MET cc_start: 0.2898 (OUTLIER) cc_final: -0.0224 (tmm)
REVERT: A  299 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6923 (mp0)
REVERT: A  370 GLU cc_start: 0.7071 (tp30) cc_final: 0.6824 (tp30)
REVERT: B   46 ARG cc_start: 0.8617 (ptm160) cc_final: 0.7656 (pmt170)
REVERT: B   59 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8584 (t80)
REVERT: B  138 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: B  217 MET cc_start: 0.8333 (ptt) cc_final: 0.8083 (pmm)
REVERT: G   18 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6519 (tm130)
REVERT: G   20 LYS cc_start: 0.7848 (pptt) cc_final: 0.7520 (ptpt)
REVERT: G   62 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6650 (tpm-80)
REVERT: N   86 LEU cc_start: 0.8441 (mt) cc_final: 0.8050 (mm)
REVERT: L   11 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8600 (mmpt)
  outliers start: 26
  outliers final: 13
  residues processed: 145
  average time/residue: 1.0667
  time to fit residues: 166.0081
Evaluate side-chains
  143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
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 B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   76 ASP
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  107 CYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   58 SER
Chi-restraints excluded: chain R residue  173 ILE
Chi-restraints excluded: chain R residue  269 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 9 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.175753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.133332 restraints weight = 11738.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 3.08
r_work: 0.3469 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3474
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3474 r_free = 0.3474    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
r_final: 0.3474
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8305  Z= 0.214
  Angle     :  0.518   6.580  11240  Z= 0.283
  Chirality :  0.041   0.142   1282
  Planarity :  0.004   0.047   1428
  Dihedral  :  4.246  55.089   1123
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 22.15 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 1014
  helix:  2.70 (0.24), residues: 413
  sheet:  0.57 (0.33), residues: 237
  loop :  0.07 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP R 258 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.011   0.000   ARG G  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6503.52 seconds
wall clock time: 112 minutes 7.98 seconds (6727.98 seconds total)