Starting phenix.real_space_refine
on Sun Apr  5 06:20:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9llf_63200/04_2026/9llf_63200.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.119
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5484      2.51       5
     N    1476      2.21       5
     O    1570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8583
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2107
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 9, 'TRANS': 255}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1865
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2610
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "M"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 576
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 65}
    Chain: "R"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'LDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.23
  Number of scatterers: 8583
  At special positions: 0
  Unit cell: (80.91, 103.23, 135.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1570      8.00
     N    1476      7.00
     C    5484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 259.5 milliseconds
  

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      45.6% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 51
    Processing helix  chain 'R' and resid 58 through 77
      removed outlier: 4.075A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA R  74 " --> pdb=" O   ASP R  70 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL R  77 " --> pdb=" O   VAL R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 86
    Processing helix  chain 'R' and resid 96 through 127
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 156
      removed outlier: 3.807A  pdb=" N   SER R 155 " --> pdb=" O   SER R 151 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE R 156 " --> pdb=" O   VAL R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 156 through 161
    Processing helix  chain 'R' and resid 191 through 203
    Processing helix  chain 'R' and resid 203 through 234
    Processing helix  chain 'R' and resid 266 through 292
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 293 through 298
      Proline residue:  R 296  - end of helix
      No H-bonds generated for 'chain 'R' and resid 293 through 298'
    Processing helix  chain 'R' and resid 309 through 322
      removed outlier: 4.344A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 322 through 332
      removed outlier: 3.616A  pdb=" N   LEU R 326 " --> pdb=" O   ALA R 322 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 344
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.531A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.772A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.789A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 4.036A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.758A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.638A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 6 through 24
      removed outlier: 4.089A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.518A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 6 through 36
    Processing helix  chain 'M' and resid 42 through 64
      removed outlier: 3.671A  pdb=" N   PHE M  48 " --> pdb=" O   MET M  44 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 66 through 71
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.528A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.549A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.591A  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: 3.685A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.903A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.159A  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 151
      removed outlier: 6.746A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.834A  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: 3.583A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.125A  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: 6.774A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.547A  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: 3.755A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.102A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1347 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.37

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1378
        1.28 -     1.42: 2309
        1.42 -     1.55: 4993
        1.55 -     1.68: 2
        1.68 -     1.81: 71
  Bond restraints: 8753
  Sorted by residual:
  bond pdb=" CA  ILE R 154 "
       pdb=" CB  ILE R 154 "
    ideal  model  delta    sigma   weight residual
    1.538  1.656 -0.118 1.28e-02 6.10e+03 8.56e+01
  bond pdb=" CA  ILE R 154 "
       pdb=" C   ILE R 154 "
    ideal  model  delta    sigma   weight residual
    1.523  1.394  0.129 1.42e-02 4.96e+03 8.29e+01
  bond pdb=" C   SER R 155 "
       pdb=" N   PHE R 156 "
    ideal  model  delta    sigma   weight residual
    1.333  1.226  0.107 1.26e-02 6.30e+03 7.24e+01
  bond pdb=" C   ILE R 154 "
       pdb=" N   SER R 155 "
    ideal  model  delta    sigma   weight residual
    1.331  1.223  0.108 1.38e-02 5.25e+03 6.07e+01
  bond pdb=" N   SER R 155 "
       pdb=" CA  SER R 155 "
    ideal  model  delta    sigma   weight residual
    1.458  1.368  0.090 1.30e-02 5.92e+03 4.76e+01
  ... (remaining 8748 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 11759
        2.27 -     4.53: 80
        4.53 -     6.80: 14
        6.80 -     9.06: 2
        9.06 -    11.33: 2
  Bond angle restraints: 11857
  Sorted by residual:
  angle pdb=" N   SER R 155 "
        pdb=" CA  SER R 155 "
        pdb=" C   SER R 155 "
      ideal   model   delta    sigma   weight residual
     113.55  124.88  -11.33 1.26e+00 6.30e-01 8.08e+01
  angle pdb=" O   VAL R 152 "
        pdb=" C   VAL R 152 "
        pdb=" N   LEU R 153 "
      ideal   model   delta    sigma   weight residual
     121.80  115.15    6.65 1.13e+00 7.83e-01 3.46e+01
  angle pdb=" C   SER R 155 "
        pdb=" CA  SER R 155 "
        pdb=" CB  SER R 155 "
      ideal   model   delta    sigma   weight residual
     109.34  101.23    8.11 1.55e+00 4.16e-01 2.73e+01
  angle pdb=" C   LEU R 153 "
        pdb=" N   ILE R 154 "
        pdb=" CA  ILE R 154 "
      ideal   model   delta    sigma   weight residual
     120.64  128.76   -8.12 1.64e+00 3.72e-01 2.45e+01
  angle pdb=" CA  VAL R 152 "
        pdb=" C   VAL R 152 "
        pdb=" N   LEU R 153 "
      ideal   model   delta    sigma   weight residual
     117.69  123.59   -5.90 1.27e+00 6.20e-01 2.16e+01
  ... (remaining 11852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 5004
       16.61 -    33.22: 178
       33.22 -    49.84: 31
       49.84 -    66.45: 5
       66.45 -    83.06: 5
  Dihedral angle restraints: 5223
    sinusoidal: 2055
      harmonic: 3168
  Sorted by residual:
  dihedral pdb=" CA  VAL R  83 "
           pdb=" C   VAL R  83 "
           pdb=" N   ALA R  84 "
           pdb=" CA  ALA R  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.03   28.97     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  TYR A 391 "
           pdb=" C   TYR A 391 "
           pdb=" N   GLU A 392 "
           pdb=" CA  GLU A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.76  -24.24     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  PHE N  27 "
           pdb=" C   PHE N  27 "
           pdb=" N   THR N  28 "
           pdb=" CA  THR N  28 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.01   21.99     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 5220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1290
       0.091 -    0.182: 71
       0.182 -    0.273: 0
       0.273 -    0.364: 0
       0.364 -    0.455: 2
  Chirality restraints: 1363
  Sorted by residual:
  chirality pdb=" CA  SER R 155 "
            pdb=" N   SER R 155 "
            pdb=" C   SER R 155 "
            pdb=" CB  SER R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.46 2.00e-01 2.50e+01 5.18e+00
  chirality pdb=" CA  LEU R 153 "
            pdb=" N   LEU R 153 "
            pdb=" C   LEU R 153 "
            pdb=" CB  LEU R 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.85e+00
  chirality pdb=" CB  THR A 285 "
            pdb=" CA  THR A 285 "
            pdb=" OG1 THR A 285 "
            pdb=" CG2 THR A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.79e-01
  ... (remaining 1360 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 152 "   -0.012 2.00e-02 2.50e+03   2.22e-02 4.95e+00
        pdb=" C   VAL R 152 "    0.039 2.00e-02 2.50e+03
        pdb=" O   VAL R 152 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU R 153 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO B 236 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 153 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   LEU R 153 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   LEU R 153 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE R 154 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 164
        2.68 -     3.23: 8138
        3.23 -     3.79: 13776
        3.79 -     4.34: 18874
        4.34 -     4.90: 31223
  Nonbonded interactions: 72175
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 246 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" ND2 ASN A 278 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   LYS R 134 "
            pdb=" OH  TYR M  33 "
     model   vdw
     2.258 3.040
  ... (remaining 72170 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.940
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
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      :  0.005   0.129   8756  Z= 0.299
  Angle     :  0.554  11.329  11863  Z= 0.320
  Chirality :  0.044   0.455   1363
  Planarity :  0.004   0.048   1490
  Dihedral  :  9.374  83.059   3152
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.34 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.26), residues: 1057
  helix:  1.88 (0.24), residues: 457
  sheet:  0.40 (0.33), residues: 225
  loop : -0.06 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.016   0.002   PHE R 288 
 TRP   0.018   0.002   TRP M  58 
 HIS   0.002   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 8753)
  covalent geometry    : angle       0.55331 (11857)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.13820 (    6)
  hydrogen bonds       : bond        0.12018 (  470)
  hydrogen bonds       : angle       5.53689 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: R  193 THR cc_start: 0.8191 (m) cc_final: 0.7965 (t)
REVERT: B  262 MET cc_start: 0.6884 (tpp) cc_final: 0.6535 (ttt)
REVERT: N   31 ASN cc_start: 0.6960 (m-40) cc_final: 0.6723 (m-40)
REVERT: M   24 LEU cc_start: 0.6473 (mt) cc_final: 0.6264 (mt)
REVERT: M   47 VAL cc_start: 0.8661 (p) cc_final: 0.8436 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.5667
  time to fit residues: 119.7350
Evaluate side-chains
  131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R  53 HIS
B  75 GLN
B 155 ASN
B 175 GLN
B 176 GLN
B 268 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.189212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.148190 restraints weight = 9992.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 2.15
r_work: 0.3583 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3471 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8756  Z= 0.130
  Angle     :  0.516   9.171  11863  Z= 0.280
  Chirality :  0.042   0.141   1363
  Planarity :  0.004   0.051   1490
  Dihedral  :  4.547  33.036   1177
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 10.86 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.26), residues: 1057
  helix:  2.22 (0.24), residues: 458
  sheet:  0.29 (0.32), residues: 224
  loop :  0.08 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N  98 
 TYR   0.015   0.001   TYR A 339 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.020   0.002   TRP M  58 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8753)
  covalent geometry    : angle       0.51526 (11857)
  SS BOND              : bond        0.00205 (    3)
  SS BOND              : angle       1.06385 (    6)
  hydrogen bonds       : bond        0.04612 (  470)
  hydrogen bonds       : angle       4.66465 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: R   25 LEU cc_start: 0.7579 (tt) cc_final: 0.7356 (tm)
REVERT: R   35 LEU cc_start: 0.8085 (mt) cc_final: 0.7767 (mm)
REVERT: R   52 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7484 (mtt90)
REVERT: A   17 LYS cc_start: 0.7145 (ptpt) cc_final: 0.6850 (mmtp)
REVERT: A  223 ASP cc_start: 0.8470 (t70) cc_final: 0.8262 (t70)
REVERT: A  283 ARG cc_start: 0.7309 (ptp-170) cc_final: 0.6452 (mmm-85)
REVERT: A  314 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6611 (tm-30)
REVERT: A  336 ARG cc_start: 0.6586 (ttp80) cc_final: 0.6332 (ttp80)
REVERT: B  137 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7470 (tpt90)
REVERT: B  217 MET cc_start: 0.7386 (ppp) cc_final: 0.7103 (pp-130)
REVERT: B  234 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.6343 (m-80)
REVERT: B  262 MET cc_start: 0.7648 (tpp) cc_final: 0.6711 (ttt)
REVERT: B  264 TYR cc_start: 0.7656 (m-80) cc_final: 0.7419 (m-80)
REVERT: B  314 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (ptm160)
REVERT: C   21 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6757 (mpm)
REVERT: N   65 LYS cc_start: 0.6443 (mtpt) cc_final: 0.6129 (mttt)
  outliers start: 24
  outliers final: 9
  residues processed: 159
  average time/residue: 0.5814
  time to fit residues: 98.1262
Evaluate side-chains
  140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   21 MET
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 67 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.183390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.139801 restraints weight = 9836.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.00
r_work: 0.3523 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8756  Z= 0.205
  Angle     :  0.593   8.647  11863  Z= 0.321
  Chirality :  0.045   0.150   1363
  Planarity :  0.005   0.053   1490
  Dihedral  :  4.895  34.982   1177
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 11.18 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.26), residues: 1057
  helix:  1.93 (0.24), residues: 455
  sheet:  0.13 (0.33), residues: 215
  loop : -0.17 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 347 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.021   0.002   PHE R 288 
 TRP   0.028   0.002   TRP M  58 
 HIS   0.004   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8753)
  covalent geometry    : angle       0.59200 (11857)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       1.59653 (    6)
  hydrogen bonds       : bond        0.05210 (  470)
  hydrogen bonds       : angle       4.71026 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.276 
Fit side-chains
REVERT: R   52 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7549 (mtt90)
REVERT: A  223 ASP cc_start: 0.8541 (t70) cc_final: 0.8304 (t70)
REVERT: A  230 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7677 (mt-10)
REVERT: A  283 ARG cc_start: 0.7412 (ptp-170) cc_final: 0.6372 (mmm-85)
REVERT: A  314 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6605 (tm-30)
REVERT: A  336 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6375 (ttp80)
REVERT: A  392 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7978 (mt-10)
REVERT: B  134 ARG cc_start: 0.6951 (ptt90) cc_final: 0.6738 (ptt-90)
REVERT: B  217 MET cc_start: 0.7421 (ppp) cc_final: 0.7116 (pp-130)
REVERT: B  234 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6315 (m-80)
REVERT: B  262 MET cc_start: 0.7614 (tpp) cc_final: 0.7082 (ttt)
REVERT: B  264 TYR cc_start: 0.7864 (m-80) cc_final: 0.7595 (m-80)
REVERT: B  314 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8326 (ptm160)
REVERT: N   65 LYS cc_start: 0.6738 (mtpt) cc_final: 0.6430 (mttt)
  outliers start: 31
  outliers final: 17
  residues processed: 152
  average time/residue: 0.5911
  time to fit residues: 95.2755
Evaluate side-chains
  145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  105 MET
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 64 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 155 ASN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.183681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139356 restraints weight = 10016.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.08
r_work: 0.3499 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8756  Z= 0.192
  Angle     :  0.580   8.761  11863  Z= 0.312
  Chirality :  0.044   0.144   1363
  Planarity :  0.005   0.051   1490
  Dihedral  :  4.902  35.190   1177
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 11.93 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.26), residues: 1057
  helix:  1.91 (0.24), residues: 449
  sheet:  0.04 (0.33), residues: 215
  loop : -0.35 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 347 
 TYR   0.017   0.002   TYR A 339 
 PHE   0.021   0.002   PHE A 212 
 TRP   0.032   0.002   TRP M  58 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 8753)
  covalent geometry    : angle       0.57949 (11857)
  SS BOND              : bond        0.00355 (    3)
  SS BOND              : angle       1.52210 (    6)
  hydrogen bonds       : bond        0.04951 (  470)
  hydrogen bonds       : angle       4.65412 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 0.261 
Fit side-chains
REVERT: R   52 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7633 (mtt90)
REVERT: R  207 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8363 (t)
REVERT: R  329 ILE cc_start: 0.8703 (mt) cc_final: 0.8467 (mm)
REVERT: A  223 ASP cc_start: 0.8601 (t70) cc_final: 0.8376 (t70)
REVERT: A  230 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7774 (mt-10)
REVERT: A  283 ARG cc_start: 0.7505 (ptp-170) cc_final: 0.7109 (ptp-110)
REVERT: A  314 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6677 (tm-30)
REVERT: B  134 ARG cc_start: 0.7042 (ptt90) cc_final: 0.6823 (ptt-90)
REVERT: B  217 MET cc_start: 0.7384 (ppp) cc_final: 0.7144 (pp-130)
REVERT: B  219 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7900 (ttm170)
REVERT: B  234 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.6276 (m-80)
REVERT: B  262 MET cc_start: 0.7737 (tpp) cc_final: 0.6829 (ttt)
REVERT: B  264 TYR cc_start: 0.7859 (m-80) cc_final: 0.7458 (m-80)
REVERT: B  314 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8311 (ptm160)
REVERT: N   65 LYS cc_start: 0.6927 (mtpt) cc_final: 0.6654 (mttt)
  outliers start: 34
  outliers final: 18
  residues processed: 152
  average time/residue: 0.5391
  time to fit residues: 87.2579
Evaluate side-chains
  147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  105 MET
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 48 optimal weight:   20.0000
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
N  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.183769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139463 restraints weight = 9925.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.07
r_work: 0.3507 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8756  Z= 0.175
  Angle     :  0.571   8.441  11863  Z= 0.306
  Chirality :  0.043   0.152   1363
  Planarity :  0.004   0.049   1490
  Dihedral  :  4.856  35.421   1177
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 12.89 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.26), residues: 1057
  helix:  1.96 (0.24), residues: 444
  sheet: -0.11 (0.33), residues: 221
  loop : -0.38 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 347 
 TYR   0.017   0.002   TYR A 339 
 PHE   0.021   0.002   PHE A 212 
 TRP   0.035   0.002   TRP M  58 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 8753)
  covalent geometry    : angle       0.56978 (11857)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       1.48862 (    6)
  hydrogen bonds       : bond        0.04787 (  470)
  hydrogen bonds       : angle       4.61040 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.238 
Fit side-chains
REVERT: R   52 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7727 (mtt90)
REVERT: R  207 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8340 (t)
REVERT: R  329 ILE cc_start: 0.8700 (mt) cc_final: 0.8476 (mm)
REVERT: A   16 GLU cc_start: 0.6108 (mp0) cc_final: 0.5847 (mp0)
REVERT: A  223 ASP cc_start: 0.8606 (t70) cc_final: 0.8365 (t70)
REVERT: A  230 GLU cc_start: 0.7931 (mt-10) cc_final: 0.6993 (mm-30)
REVERT: A  283 ARG cc_start: 0.7462 (ptp-170) cc_final: 0.7098 (ptp-110)
REVERT: A  314 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6621 (tm-30)
REVERT: A  336 ARG cc_start: 0.6724 (ttp80) cc_final: 0.6399 (ttp80)
REVERT: B  134 ARG cc_start: 0.7024 (ptt90) cc_final: 0.6809 (ptt-90)
REVERT: B  214 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7826 (mmt90)
REVERT: B  217 MET cc_start: 0.7387 (ppp) cc_final: 0.7151 (pp-130)
REVERT: B  219 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7971 (ttm170)
REVERT: B  234 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.6238 (m-80)
REVERT: B  262 MET cc_start: 0.7731 (tpp) cc_final: 0.7040 (ttt)
REVERT: B  264 TYR cc_start: 0.7797 (m-80) cc_final: 0.7435 (m-80)
REVERT: N   65 LYS cc_start: 0.7025 (mtpt) cc_final: 0.6801 (mttt)
  outliers start: 33
  outliers final: 24
  residues processed: 158
  average time/residue: 0.5478
  time to fit residues: 92.1070
Evaluate side-chains
  155 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  105 MET
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  193 THR
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 259 GLN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.185427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141630 restraints weight = 9905.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.06
r_work: 0.3543 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8756  Z= 0.138
  Angle     :  0.540   8.632  11863  Z= 0.290
  Chirality :  0.042   0.162   1363
  Planarity :  0.004   0.049   1490
  Dihedral  :  4.688  34.385   1177
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 13.21 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1057
  helix:  2.13 (0.24), residues: 445
  sheet: -0.15 (0.33), residues: 221
  loop : -0.39 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 347 
 TYR   0.016   0.002   TYR A 339 
 PHE   0.020   0.002   PHE A 212 
 TRP   0.036   0.002   TRP M  58 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8753)
  covalent geometry    : angle       0.53965 (11857)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       1.28042 (    6)
  hydrogen bonds       : bond        0.04401 (  470)
  hydrogen bonds       : angle       4.48834 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 0.337 
Fit side-chains
REVERT: R   35 LEU cc_start: 0.8138 (mt) cc_final: 0.7846 (mm)
REVERT: R   52 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7782 (mtt90)
REVERT: R  329 ILE cc_start: 0.8720 (mt) cc_final: 0.8503 (mm)
REVERT: A   16 GLU cc_start: 0.6101 (mp0) cc_final: 0.5845 (mp0)
REVERT: A   38 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7245 (mmt180)
REVERT: A  223 ASP cc_start: 0.8602 (t70) cc_final: 0.8364 (t70)
REVERT: A  230 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7545 (mt-10)
REVERT: A  283 ARG cc_start: 0.7357 (ptp-170) cc_final: 0.7108 (ptp-110)
REVERT: A  314 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6602 (tm-30)
REVERT: A  336 ARG cc_start: 0.6646 (ttp80) cc_final: 0.5948 (ttt-90)
REVERT: A  386 MET cc_start: 0.8345 (ttp) cc_final: 0.8084 (ttp)
REVERT: B  214 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7778 (mmt90)
REVERT: B  217 MET cc_start: 0.7384 (ppp) cc_final: 0.7152 (pp-130)
REVERT: B  219 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7957 (ttm170)
REVERT: B  234 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.6181 (m-80)
REVERT: B  262 MET cc_start: 0.7703 (tpp) cc_final: 0.6959 (ttt)
REVERT: B  264 TYR cc_start: 0.7752 (m-80) cc_final: 0.7436 (m-80)
REVERT: B  314 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8307 (ptm160)
REVERT: N   65 LYS cc_start: 0.7057 (mtpt) cc_final: 0.6857 (mttt)
REVERT: M   46 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7917 (ttmp)
  outliers start: 37
  outliers final: 23
  residues processed: 161
  average time/residue: 0.5898
  time to fit residues: 100.9839
Evaluate side-chains
  157 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain M residue   46 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    0.1980
   chunk 92 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.185717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.141668 restraints weight = 9945.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.07
r_work: 0.3507 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8756  Z= 0.132
  Angle     :  0.536   9.164  11863  Z= 0.285
  Chirality :  0.042   0.133   1363
  Planarity :  0.004   0.048   1490
  Dihedral  :  4.609  34.494   1177
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.84 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.26), residues: 1057
  helix:  2.23 (0.24), residues: 444
  sheet: -0.11 (0.34), residues: 219
  loop : -0.38 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG N 105 
 TYR   0.015   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 212 
 TRP   0.038   0.002   TRP M  58 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8753)
  covalent geometry    : angle       0.53544 (11857)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       1.20243 (    6)
  hydrogen bonds       : bond        0.04299 (  470)
  hydrogen bonds       : angle       4.45290 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.276 
Fit side-chains
REVERT: R   35 LEU cc_start: 0.8099 (mt) cc_final: 0.7833 (mm)
REVERT: R   52 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7764 (mtt90)
REVERT: R  223 LYS cc_start: 0.8028 (mttm) cc_final: 0.7327 (ttpt)
REVERT: R  329 ILE cc_start: 0.8698 (mt) cc_final: 0.8481 (mm)
REVERT: A   16 GLU cc_start: 0.5954 (mp0) cc_final: 0.5690 (mp0)
REVERT: A   38 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7289 (mmt180)
REVERT: A  223 ASP cc_start: 0.8590 (t70) cc_final: 0.8370 (t70)
REVERT: A  283 ARG cc_start: 0.7326 (ptp-170) cc_final: 0.7073 (ptp-110)
REVERT: A  314 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6634 (tm-30)
REVERT: A  336 ARG cc_start: 0.6552 (ttp80) cc_final: 0.5918 (ttt180)
REVERT: A  386 MET cc_start: 0.8381 (ttp) cc_final: 0.8153 (ttp)
REVERT: B  134 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6863 (ptt180)
REVERT: B  214 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7773 (mmt90)
REVERT: B  217 MET cc_start: 0.7355 (ppp) cc_final: 0.7109 (pp-130)
REVERT: B  219 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7977 (ttm170)
REVERT: B  234 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6155 (m-80)
REVERT: B  262 MET cc_start: 0.7767 (tpp) cc_final: 0.7069 (ttt)
REVERT: B  264 TYR cc_start: 0.7733 (m-80) cc_final: 0.7409 (m-80)
REVERT: B  314 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8274 (ptm160)
REVERT: B  340 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.7282 (m-40)
REVERT: N   65 LYS cc_start: 0.7188 (mtpt) cc_final: 0.6935 (mttt)
REVERT: M   46 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7848 (ttmp)
REVERT: M   58 TRP cc_start: 0.7883 (t60) cc_final: 0.7346 (t-100)
  outliers start: 32
  outliers final: 17
  residues processed: 156
  average time/residue: 0.5777
  time to fit residues: 95.7866
Evaluate side-chains
  149 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   52 ARG
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain M residue   46 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 14 optimal weight:    0.3980
   chunk 100 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0670
   chunk 39 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 230 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.185829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141768 restraints weight = 9778.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.08
r_work: 0.3543 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8756  Z= 0.137
  Angle     :  0.558  11.894  11863  Z= 0.296
  Chirality :  0.042   0.177   1363
  Planarity :  0.004   0.047   1490
  Dihedral  :  4.620  34.582   1177
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.16 %
    Favored  : 82.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.26), residues: 1057
  helix:  2.20 (0.24), residues: 445
  sheet: -0.11 (0.33), residues: 220
  loop : -0.36 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 347 
 TYR   0.015   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 212 
 TRP   0.035   0.002   TRP M  58 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8753)
  covalent geometry    : angle       0.55770 (11857)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       1.23923 (    6)
  hydrogen bonds       : bond        0.04302 (  470)
  hydrogen bonds       : angle       4.46389 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.358 
Fit side-chains
REVERT: R   35 LEU cc_start: 0.8145 (mt) cc_final: 0.7887 (mm)
REVERT: R  223 LYS cc_start: 0.8077 (mttm) cc_final: 0.7400 (ttpt)
REVERT: R  329 ILE cc_start: 0.8718 (mt) cc_final: 0.8510 (mm)
REVERT: A   16 GLU cc_start: 0.5956 (mp0) cc_final: 0.5729 (mp0)
REVERT: A   28 LYS cc_start: 0.6997 (pptt) cc_final: 0.6320 (mttt)
REVERT: A   38 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7369 (mmt180)
REVERT: A  223 ASP cc_start: 0.8623 (t70) cc_final: 0.8405 (t70)
REVERT: A  314 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6590 (tm-30)
REVERT: A  336 ARG cc_start: 0.6470 (ttp80) cc_final: 0.6246 (ttp80)
REVERT: A  386 MET cc_start: 0.8436 (ttp) cc_final: 0.8220 (ttp)
REVERT: B  214 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7846 (mmt90)
REVERT: B  217 MET cc_start: 0.7392 (ppp) cc_final: 0.7154 (pp-130)
REVERT: B  219 ARG cc_start: 0.8331 (ttm170) cc_final: 0.8027 (ttm170)
REVERT: B  234 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.6198 (m-80)
REVERT: B  262 MET cc_start: 0.7731 (tpp) cc_final: 0.7053 (ttt)
REVERT: B  264 TYR cc_start: 0.7748 (m-80) cc_final: 0.7412 (m-80)
REVERT: B  314 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8289 (ptm160)
REVERT: N   31 ASN cc_start: 0.7336 (m-40) cc_final: 0.7099 (m-40)
REVERT: N   65 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6953 (mttt)
REVERT: M   46 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7728 (ttmp)
  outliers start: 31
  outliers final: 21
  residues processed: 149
  average time/residue: 0.5841
  time to fit residues: 92.5416
Evaluate side-chains
  149 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   39 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue   73 VAL
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain M residue   46 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0770
   chunk 76 optimal weight:    0.9990
   chunk 99 optimal weight:    0.4980
   chunk 49 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 39 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.187495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.143777 restraints weight = 9833.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.06
r_work: 0.3561 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8756  Z= 0.114
  Angle     :  0.535  10.732  11863  Z= 0.284
  Chirality :  0.042   0.161   1363
  Planarity :  0.004   0.046   1490
  Dihedral  :  4.467  34.031   1177
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.23 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.26), residues: 1057
  helix:  2.36 (0.24), residues: 444
  sheet: -0.07 (0.34), residues: 219
  loop : -0.33 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N 105 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 212 
 TRP   0.041   0.002   TRP M  58 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8753)
  covalent geometry    : angle       0.53473 (11857)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       1.00996 (    6)
  hydrogen bonds       : bond        0.04001 (  470)
  hydrogen bonds       : angle       4.35889 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7582 (tt)
REVERT: R  223 LYS cc_start: 0.8024 (mttm) cc_final: 0.7361 (ttpt)
REVERT: R  329 ILE cc_start: 0.8705 (mt) cc_final: 0.8501 (mm)
REVERT: A   28 LYS cc_start: 0.6932 (pptt) cc_final: 0.6294 (mttt)
REVERT: A   38 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7313 (mmt180)
REVERT: A  223 ASP cc_start: 0.8602 (t70) cc_final: 0.8391 (t70)
REVERT: A  283 ARG cc_start: 0.7461 (ptp-170) cc_final: 0.6058 (mmm-85)
REVERT: A  314 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6491 (tm-30)
REVERT: A  386 MET cc_start: 0.8399 (ttp) cc_final: 0.8180 (ttp)
REVERT: B  134 ARG cc_start: 0.6998 (ptt-90) cc_final: 0.5946 (ppt90)
REVERT: B  214 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7981 (mmt90)
REVERT: B  217 MET cc_start: 0.7342 (ppp) cc_final: 0.7100 (pp-130)
REVERT: B  219 ARG cc_start: 0.8332 (ttm170) cc_final: 0.8088 (ttm170)
REVERT: B  234 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6096 (m-80)
REVERT: B  262 MET cc_start: 0.7801 (tpp) cc_final: 0.7188 (ttt)
REVERT: B  264 TYR cc_start: 0.7703 (m-80) cc_final: 0.7414 (m-80)
REVERT: B  314 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8148 (ptm160)
REVERT: N   34 MET cc_start: 0.7458 (tpp) cc_final: 0.6942 (mmt)
REVERT: N   65 LYS cc_start: 0.7191 (mtpt) cc_final: 0.6968 (mttt)
REVERT: M   58 TRP cc_start: 0.7872 (t60) cc_final: 0.7511 (t-100)
  outliers start: 23
  outliers final: 16
  residues processed: 143
  average time/residue: 0.5683
  time to fit residues: 86.4045
Evaluate side-chains
  143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   31 SER
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.188083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144625 restraints weight = 9805.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 2.04
r_work: 0.3563 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8756  Z= 0.115
  Angle     :  0.551  12.734  11863  Z= 0.290
  Chirality :  0.042   0.189   1363
  Planarity :  0.004   0.046   1490
  Dihedral  :  4.424  34.109   1177
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.97 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.26), residues: 1057
  helix:  2.41 (0.24), residues: 445
  sheet: -0.05 (0.34), residues: 224
  loop : -0.32 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 347 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 212 
 TRP   0.040   0.002   TRP M  58 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8753)
  covalent geometry    : angle       0.55096 (11857)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       0.99300 (    6)
  hydrogen bonds       : bond        0.03971 (  470)
  hydrogen bonds       : angle       4.33499 ( 1347)

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

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

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2114 Ramachandran restraints generated.
    1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: R  161 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7591 (tt)
REVERT: R  223 LYS cc_start: 0.8024 (mttm) cc_final: 0.7363 (ttpt)
REVERT: R  329 ILE cc_start: 0.8711 (mt) cc_final: 0.8511 (mm)
REVERT: A   38 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7312 (mmt180)
REVERT: A  314 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6467 (tm-30)
REVERT: A  336 ARG cc_start: 0.6521 (ttp80) cc_final: 0.5838 (ttp80)
REVERT: A  386 MET cc_start: 0.8400 (ttp) cc_final: 0.8190 (ttp)
REVERT: B  214 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7993 (mmt90)
REVERT: B  219 ARG cc_start: 0.8338 (ttm170) cc_final: 0.8062 (ttm170)
REVERT: B  234 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.6080 (m-80)
REVERT: B  262 MET cc_start: 0.7719 (tpp) cc_final: 0.7104 (ttt)
REVERT: B  264 TYR cc_start: 0.7697 (m-80) cc_final: 0.7407 (m-80)
REVERT: B  314 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8148 (ptm160)
REVERT: N   34 MET cc_start: 0.7489 (tpp) cc_final: 0.7053 (mmt)
REVERT: N   65 LYS cc_start: 0.7180 (mtpt) cc_final: 0.6943 (mttt)
REVERT: M   58 TRP cc_start: 0.7864 (t60) cc_final: 0.7511 (t-100)
  outliers start: 20
  outliers final: 15
  residues processed: 141
  average time/residue: 0.5688
  time to fit residues: 85.5118
Evaluate side-chains
  148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   48 VAL
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  333 PHE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   85 SER
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    0.1980
   chunk 103 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.187091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143592 restraints weight = 9795.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.05
r_work: 0.3552 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8756  Z= 0.124
  Angle     :  0.538   8.822  11863  Z= 0.290
  Chirality :  0.042   0.160   1363
  Planarity :  0.004   0.046   1490
  Dihedral  :  4.462  34.391   1177
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.19 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.26), residues: 1057
  helix:  2.43 (0.24), residues: 444
  sheet: -0.06 (0.34), residues: 219
  loop : -0.36 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG N 105 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 212 
 TRP   0.039   0.002   TRP M  58 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8753)
  covalent geometry    : angle       0.53746 (11857)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       1.04924 (    6)
  hydrogen bonds       : bond        0.04065 (  470)
  hydrogen bonds       : angle       4.31493 ( 1347)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3790.78 seconds
wall clock time: 65 minutes 7.76 seconds (3907.76 seconds total)