Starting phenix.real_space_refine
on Wed Sep 17 10:37:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zce_39927/09_2025/8zce_39927.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 251 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5054      2.51       5
     N    1375      2.21       5
     O    1484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7963
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1797
          Classifications: {'peptide': 224}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 217}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 64
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "B"
      Number of atoms: 2508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2508
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 6, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 76
    Chain: "C"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 395
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "N"
      Number of atoms: 947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 947
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 2316
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2316
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 282}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 42
  Time building chain proxies: 2.00, per 1000 atoms: 0.25
  Number of scatterers: 7963
  At special positions: 0
  Unit cell: (84.24, 94.64, 132.08, 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      50     16.00
     O    1484      8.00
     N    1375      7.00
     C    5054      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R   9 " - pdb=" SG  CYS R 258 " 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: 0.66
  Conformation dependent library (CDL) restraints added in 441.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1954

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      40.2% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 3.747A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 61
      removed outlier: 3.744A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 3.865A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 4.287A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.983A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 11 through 25
      removed outlier: 3.599A  pdb=" N   ILE C  25 " --> pdb=" O   MET C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 4.424A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 14 through 17
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 3.712A  pdb=" N   LEU R  32 " --> pdb=" O   ILE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 51 through 79
      removed outlier: 3.891A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 98
      removed outlier: 4.042A  pdb=" N   PHE R  95 " --> pdb=" O   LYS R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 120
    Processing helix  chain 'R' and resid 130 through 149
    Processing helix  chain 'R' and resid 150 through 155
      removed outlier: 3.983A  pdb=" N   PHE R 154 " --> pdb=" O   SER R 150 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   HIS R 155 " --> pdb=" O   ALA R 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 150 through 155'
    Processing helix  chain 'R' and resid 175 through 188
    Processing helix  chain 'R' and resid 190 through 211
    Processing helix  chain 'R' and resid 215 through 254
      removed outlier: 4.052A  pdb=" N   VAL R 233 " --> pdb=" O   LEU R 229 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 259 through 276
      removed outlier: 4.087A  pdb=" N   ARG R 263 " --> pdb=" O   GLY R 259 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   SER R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ALA R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 287
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 301
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.719A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.670A  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: 3.798A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.248A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.759A  pdb=" N   LEU B 152 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.771A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.714A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.559A  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: 3.648A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.589A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 5
      removed outlier: 3.518A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.825A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLN N  39 " --> pdb=" O   VAL N  93 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR N  95 " --> pdb=" O   VAL N  37 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 17 through 19
    Processing sheet with id=AB3, first strand: chain 'R' and resid 159 through 160

    392 hydrogen bonds defined for protein.
    1122 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: 1.23

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2628
        1.34 -     1.46: 1991
        1.46 -     1.58: 3453
        1.58 -     1.70: 0
        1.70 -     1.82: 67
  Bond restraints: 8139
  Sorted by residual:
  bond pdb=" N   ILE B 270 "
       pdb=" CA  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 9.30e-03 1.16e+04 1.78e+01
  bond pdb=" CA  GLN N  39 "
       pdb=" CB  GLN N  39 "
    ideal  model  delta    sigma   weight residual
    1.528  1.577 -0.049 1.51e-02 4.39e+03 1.05e+01
  bond pdb=" N   ARG A 232 "
       pdb=" CA  ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.35e-02 5.49e+03 6.30e+00
  bond pdb=" C   LEU R  70 "
       pdb=" N   PRO R  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.36e-02 5.41e+03 2.37e+00
  bond pdb=" C   ILE B 270 "
       pdb=" O   ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.232  1.251 -0.019 1.30e-02 5.92e+03 2.24e+00
  ... (remaining 8134 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 10844
        2.00 -     3.99: 197
        3.99 -     5.99: 21
        5.99 -     7.99: 9
        7.99 -     9.98: 1
  Bond angle restraints: 11072
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  106.56    6.64 9.60e-01 1.09e+00 4.78e+01
  angle pdb=" CB  LYS A 271 "
        pdb=" CG  LYS A 271 "
        pdb=" CD  LYS A 271 "
      ideal   model   delta    sigma   weight residual
     111.30  103.69    7.61 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  PRO R 173 "
        pdb=" N   PRO R 173 "
        pdb=" CD  PRO R 173 "
      ideal   model   delta    sigma   weight residual
     112.00  107.62    4.38 1.40e+00 5.10e-01 9.79e+00
  angle pdb=" CD  LYS A 271 "
        pdb=" CE  LYS A 271 "
        pdb=" NZ  LYS A 271 "
      ideal   model   delta    sigma   weight residual
     111.90  101.92    9.98 3.20e+00 9.77e-02 9.74e+00
  angle pdb=" N   ILE A 308 "
        pdb=" CA  ILE A 308 "
        pdb=" C   ILE A 308 "
      ideal   model   delta    sigma   weight residual
     111.62  109.17    2.45 7.90e-01 1.60e+00 9.65e+00
  ... (remaining 11067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.26: 4052
       13.26 -    26.52: 451
       26.52 -    39.77: 176
       39.77 -    53.03: 62
       53.03 -    66.29: 37
  Dihedral angle restraints: 4778
    sinusoidal: 1755
      harmonic: 3023
  Sorted by residual:
  dihedral pdb=" CB  CYS R   9 "
           pdb=" SG  CYS R   9 "
           pdb=" SG  CYS R 258 "
           pdb=" CB  CYS R 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.42   37.42     1      1.00e+01 1.00e-02 1.98e+01
  dihedral pdb=" CA  PHE R 172 "
           pdb=" C   PHE R 172 "
           pdb=" N   PRO R 173 "
           pdb=" CA  PRO R 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.10   19.90     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CG  ARG R 216 "
           pdb=" CD  ARG R 216 "
           pdb=" NE  ARG R 216 "
           pdb=" CZ  ARG R 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -36.73  -53.27     2      1.50e+01 4.44e-03 1.37e+01
  ... (remaining 4775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 937
       0.045 -    0.091: 252
       0.091 -    0.136: 62
       0.136 -    0.182: 2
       0.182 -    0.227: 1
  Chirality restraints: 1254
  Sorted by residual:
  chirality pdb=" CA  ILE B 270 "
            pdb=" N   ILE B 270 "
            pdb=" C   ILE B 270 "
            pdb=" CB  ILE B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  LYS A 271 "
            pdb=" N   LYS A 271 "
            pdb=" C   LYS A 271 "
            pdb=" CB  LYS A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CB  ILE B  18 "
            pdb=" CA  ILE B  18 "
            pdb=" CG1 ILE B  18 "
            pdb=" CG2 ILE B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.09e-01
  ... (remaining 1251 not shown)

  Planarity restraints: 1425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 172 "    0.069 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO R 173 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO R 173 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO R 173 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS N  99 "    0.043 5.00e-02 4.00e+02   6.56e-02 6.89e+00
        pdb=" N   PRO N 100 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO N 100 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO N 100 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  99 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.36e+00
        pdb=" C   THR R  99 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   THR R  99 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN R 100 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1422 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 169
        2.68 -     3.23: 7972
        3.23 -     3.79: 13355
        3.79 -     4.34: 17856
        4.34 -     4.90: 29087
  Nonbonded interactions: 68439
  Sorted by model distance:
  nonbonded pdb=" OG  SER R  13 "
            pdb=" OG  SER R 266 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" O   ALA R 267 "
            pdb=" OG  SER R 271 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" NH1 ARG N  67 "
            pdb=" O   SER N  85 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OE2 GLU B 226 "
            pdb=" OH  TYR N  32 "
     model   vdw
     2.244 3.040
  ... (remaining 68434 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
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      :  0.004   0.065   8140  Z= 0.192
  Angle     :  0.661   9.985  11074  Z= 0.374
  Chirality :  0.043   0.227   1254
  Planarity :  0.005   0.103   1425
  Dihedral  : 15.439  66.291   2821
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 24.09 %
    Favored  : 75.55 %
  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 aren not related in a simple way.
  whole: -0.37 (0.26), residues: 1023
  helix:  1.37 (0.26), residues: 389
  sheet: -0.36 (0.40), residues: 188
  loop : -1.69 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R 216 
 TYR   0.026   0.002   TYR N 115 
 PHE   0.031   0.002   PHE R 169 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 8139)
  covalent geometry    : angle       0.66133 (11072)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.48289 (    2)
  hydrogen bonds       : bond        0.16431 (  392)
  hydrogen bonds       : angle       6.23893 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 129
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  212 ASP cc_start: 0.6773 (t0) cc_final: 0.6531 (t0)
REVERT: R  102 TYR cc_start: 0.7506 (m-80) cc_final: 0.7222 (m-80)
REVERT: R  155 HIS cc_start: 0.6212 (m90) cc_final: 0.5843 (m90)
REVERT: R  169 PHE cc_start: 0.6048 (t80) cc_final: 0.5505 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 130
  average time/residue: 0.1223
  time to fit residues: 20.3337
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue    9 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.1980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
A 362 HIS
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.168023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.151291 restraints weight = 11024.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.81
r_work: 0.3881 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8140  Z= 0.165
  Angle     :  0.586   7.460  11074  Z= 0.314
  Chirality :  0.042   0.128   1254
  Planarity :  0.005   0.068   1425
  Dihedral  :  4.803  50.675   1127
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.05 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.26), residues: 1023
  helix:  1.64 (0.26), residues: 390
  sheet: -0.58 (0.37), residues: 200
  loop : -1.65 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 347 
 TYR   0.014   0.002   TYR R  76 
 PHE   0.020   0.002   PHE R 107 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.006   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8139)
  covalent geometry    : angle       0.58641 (11072)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.55009 (    2)
  hydrogen bonds       : bond        0.04613 (  392)
  hydrogen bonds       : angle       4.88727 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 LEU cc_start: 0.8172 (mt) cc_final: 0.7969 (mt)
REVERT: A  299 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5297 (pp20)
REVERT: B  212 ASP cc_start: 0.6778 (t70) cc_final: 0.6504 (t0)
REVERT: B  221 THR cc_start: 0.7802 (m) cc_final: 0.7592 (m)
REVERT: B  234 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7801 (m-80)
REVERT: B  262 MET cc_start: 0.7640 (tpt) cc_final: 0.7425 (tpt)
REVERT: B  283 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6916 (tpt-90)
REVERT: B  314 ARG cc_start: 0.7162 (ttt90) cc_final: 0.6913 (ttt90)
REVERT: R  155 HIS cc_start: 0.6479 (m90) cc_final: 0.5842 (m90)
REVERT: R  169 PHE cc_start: 0.6317 (t80) cc_final: 0.5693 (t80)
REVERT: R  223 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7820 (ttmm)
REVERT: R  277 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7188 (mt)
  outliers start: 26
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1046
  time to fit residues: 20.1830
Evaluate side-chains
  144 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   89 SER
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 4 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0670
   chunk 80 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.168375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151638 restraints weight = 10996.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 1.82
r_work: 0.3888 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8140  Z= 0.136
  Angle     :  0.544   6.626  11074  Z= 0.291
  Chirality :  0.041   0.143   1254
  Planarity :  0.004   0.065   1425
  Dihedral  :  4.564  50.402   1125
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.61 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.26), residues: 1023
  helix:  1.80 (0.26), residues: 390
  sheet: -0.59 (0.36), residues: 205
  loop : -1.61 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 216 
 TYR   0.016   0.001   TYR R  76 
 PHE   0.016   0.002   PHE R  93 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8139)
  covalent geometry    : angle       0.54349 (11072)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.61231 (    2)
  hydrogen bonds       : bond        0.04264 (  392)
  hydrogen bonds       : angle       4.67011 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6486 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5188 (pp20)
REVERT: B  125 ASN cc_start: 0.7600 (t0) cc_final: 0.7299 (t0)
REVERT: B  212 ASP cc_start: 0.6731 (t70) cc_final: 0.6457 (t0)
REVERT: B  234 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7757 (m-80)
REVERT: B  262 MET cc_start: 0.7491 (tpt) cc_final: 0.7176 (tpt)
REVERT: B  314 ARG cc_start: 0.7206 (ttt90) cc_final: 0.6894 (ttt90)
REVERT: N   80 TYR cc_start: 0.7688 (m-80) cc_final: 0.7438 (m-80)
REVERT: R  155 HIS cc_start: 0.6455 (m90) cc_final: 0.5848 (m90)
REVERT: R  169 PHE cc_start: 0.6217 (t80) cc_final: 0.5536 (t80)
REVERT: R  223 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7777 (ttmm)
  outliers start: 32
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1091
  time to fit residues: 22.3213
Evaluate side-chains
  147 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   50 ASP
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   89 SER
Chi-restraints excluded: chain R residue  264 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0020
   chunk 65 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 93 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.167155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.150229 restraints weight = 11148.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 1.84
r_work: 0.3866 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8140  Z= 0.171
  Angle     :  0.562   6.655  11074  Z= 0.300
  Chirality :  0.042   0.139   1254
  Planarity :  0.004   0.064   1425
  Dihedral  :  4.606  48.289   1125
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.10 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1023
  helix:  1.72 (0.26), residues: 390
  sheet: -0.49 (0.36), residues: 198
  loop : -1.64 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 216 
 TYR   0.020   0.002   TYR R  76 
 PHE   0.017   0.002   PHE R 107 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8139)
  covalent geometry    : angle       0.56224 (11072)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.66905 (    2)
  hydrogen bonds       : bond        0.04363 (  392)
  hydrogen bonds       : angle       4.64919 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 140
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.6664 (pp30) cc_final: 0.6422 (pp30)
REVERT: A   20 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6499 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5387 (pp20)
REVERT: A  384 GLN cc_start: 0.6928 (tt0) cc_final: 0.6720 (tt0)
REVERT: B  125 ASN cc_start: 0.7582 (t0) cc_final: 0.7292 (t0)
REVERT: B  212 ASP cc_start: 0.6821 (t70) cc_final: 0.6540 (t0)
REVERT: B  234 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7753 (m-80)
REVERT: B  262 MET cc_start: 0.7472 (tpt) cc_final: 0.7258 (tpt)
REVERT: B  314 ARG cc_start: 0.7269 (ttt90) cc_final: 0.6929 (ttt90)
REVERT: C   15 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7420 (tm)
REVERT: N   80 TYR cc_start: 0.7656 (m-80) cc_final: 0.7383 (m-80)
REVERT: R   52 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6912 (mp)
REVERT: R  155 HIS cc_start: 0.6531 (m90) cc_final: 0.5938 (m90)
REVERT: R  169 PHE cc_start: 0.6326 (t80) cc_final: 0.5649 (t80)
REVERT: R  223 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7829 (ttmm)
REVERT: R  277 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7215 (mt)
  outliers start: 34
  outliers final: 20
  residues processed: 163
  average time/residue: 0.1095
  time to fit residues: 23.4533
Evaluate side-chains
  163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   89 SER
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0030
   chunk 20 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0970
   chunk 16 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.168396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.151522 restraints weight = 11066.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 1.84
r_work: 0.3890 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8140  Z= 0.122
  Angle     :  0.523   6.715  11074  Z= 0.279
  Chirality :  0.041   0.136   1254
  Planarity :  0.004   0.063   1425
  Dihedral  :  4.462  49.107   1125
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 20.80 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.26), residues: 1023
  helix:  1.96 (0.26), residues: 391
  sheet: -0.47 (0.36), residues: 196
  loop : -1.62 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 216 
 TYR   0.016   0.001   TYR R  76 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8139)
  covalent geometry    : angle       0.52319 (11072)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.63583 (    2)
  hydrogen bonds       : bond        0.03918 (  392)
  hydrogen bonds       : angle       4.46515 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.6625 (pp30) cc_final: 0.6383 (pp30)
REVERT: A   20 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6456 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5275 (pp20)
REVERT: A  384 GLN cc_start: 0.6927 (tt0) cc_final: 0.6721 (tt0)
REVERT: B  125 ASN cc_start: 0.7471 (t0) cc_final: 0.7239 (t0)
REVERT: B  212 ASP cc_start: 0.6703 (t70) cc_final: 0.6422 (t0)
REVERT: B  234 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7800 (m-80)
REVERT: B  255 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6809 (mt)
REVERT: B  314 ARG cc_start: 0.7297 (ttt90) cc_final: 0.7059 (ttt90)
REVERT: C   15 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7432 (tm)
REVERT: N   80 TYR cc_start: 0.7653 (m-80) cc_final: 0.7385 (m-80)
REVERT: R  155 HIS cc_start: 0.6530 (m90) cc_final: 0.5978 (m90)
REVERT: R  169 PHE cc_start: 0.6183 (t80) cc_final: 0.5465 (t80)
REVERT: R  277 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7197 (mt)
  outliers start: 34
  outliers final: 20
  residues processed: 162
  average time/residue: 0.1024
  time to fit residues: 22.0009
Evaluate side-chains
  160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  82 ASN
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.165910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.148944 restraints weight = 10973.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 1.82
r_work: 0.3854 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8140  Z= 0.185
  Angle     :  0.569   6.741  11074  Z= 0.303
  Chirality :  0.043   0.133   1254
  Planarity :  0.004   0.066   1425
  Dihedral  :  4.575  46.154   1125
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 20.68 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.26), residues: 1023
  helix:  1.76 (0.26), residues: 390
  sheet: -0.67 (0.36), residues: 200
  loop : -1.65 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 216 
 TYR   0.022   0.002   TYR R  76 
 PHE   0.018   0.002   PHE B 235 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8139)
  covalent geometry    : angle       0.56891 (11072)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.71387 (    2)
  hydrogen bonds       : bond        0.04348 (  392)
  hydrogen bonds       : angle       4.58956 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.6643 (pp30) cc_final: 0.6422 (pp30)
REVERT: A   20 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6495 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5367 (pp20)
REVERT: B  125 ASN cc_start: 0.7564 (t0) cc_final: 0.7332 (t0)
REVERT: B  212 ASP cc_start: 0.6787 (t70) cc_final: 0.6491 (t0)
REVERT: B  234 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7812 (m-80)
REVERT: B  255 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6780 (mt)
REVERT: B  314 ARG cc_start: 0.7321 (ttt90) cc_final: 0.7075 (ttt90)
REVERT: C   15 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (tm)
REVERT: N   80 TYR cc_start: 0.7644 (m-80) cc_final: 0.7315 (m-80)
REVERT: R   52 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6936 (mp)
REVERT: R  155 HIS cc_start: 0.6566 (m90) cc_final: 0.6259 (m-70)
REVERT: R  169 PHE cc_start: 0.6360 (t80) cc_final: 0.5633 (t80)
REVERT: R  277 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7202 (mt)
  outliers start: 41
  outliers final: 26
  residues processed: 164
  average time/residue: 0.1098
  time to fit residues: 23.6962
Evaluate side-chains
  167 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   15 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 92 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.166365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.149387 restraints weight = 11021.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 1.83
r_work: 0.3862 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3720 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8140  Z= 0.158
  Angle     :  0.555   6.740  11074  Z= 0.296
  Chirality :  0.042   0.164   1254
  Planarity :  0.004   0.065   1425
  Dihedral  :  4.569  47.563   1125
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 21.17 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.26), residues: 1023
  helix:  1.76 (0.26), residues: 392
  sheet: -0.55 (0.37), residues: 200
  loop : -1.69 (0.27), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 216 
 TYR   0.023   0.002   TYR N 115 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8139)
  covalent geometry    : angle       0.55460 (11072)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.65972 (    2)
  hydrogen bonds       : bond        0.04179 (  392)
  hydrogen bonds       : angle       4.54980 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLN cc_start: 0.6643 (pp30) cc_final: 0.6425 (pp30)
REVERT: A   20 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6522 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5309 (pp20)
REVERT: B  125 ASN cc_start: 0.7480 (t0) cc_final: 0.7252 (t0)
REVERT: B  212 ASP cc_start: 0.6752 (t70) cc_final: 0.6439 (t0)
REVERT: B  234 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7814 (m-80)
REVERT: B  283 ARG cc_start: 0.7430 (tpp80) cc_final: 0.7103 (tpp80)
REVERT: B  314 ARG cc_start: 0.7418 (ttt90) cc_final: 0.7168 (ttt90)
REVERT: C   15 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7445 (tm)
REVERT: N   80 TYR cc_start: 0.7639 (m-80) cc_final: 0.7317 (m-80)
REVERT: R    9 CYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5488 (m)
REVERT: R  155 HIS cc_start: 0.6596 (m90) cc_final: 0.6294 (m-70)
REVERT: R  169 PHE cc_start: 0.6420 (t80) cc_final: 0.5623 (t80)
REVERT: R  277 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7226 (mt)
  outliers start: 41
  outliers final: 26
  residues processed: 161
  average time/residue: 0.1089
  time to fit residues: 23.1532
Evaluate side-chains
  161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   15 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0870
   chunk 11 optimal weight:    0.4980
   chunk 80 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 GLN
B 293 ASN
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 241 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.166716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.149785 restraints weight = 11087.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 1.83
r_work: 0.3865 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6900
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8140  Z= 0.154
  Angle     :  0.555   6.746  11074  Z= 0.297
  Chirality :  0.042   0.204   1254
  Planarity :  0.004   0.065   1425
  Dihedral  :  4.528  46.175   1125
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 21.17 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.26), residues: 1023
  helix:  1.77 (0.26), residues: 392
  sheet: -0.56 (0.36), residues: 200
  loop : -1.68 (0.27), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 216 
 TYR   0.021   0.002   TYR N 115 
 PHE   0.016   0.002   PHE R 172 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8139)
  covalent geometry    : angle       0.55491 (11072)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.59881 (    2)
  hydrogen bonds       : bond        0.04151 (  392)
  hydrogen bonds       : angle       4.52621 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6532 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5254 (pp20)
REVERT: B  125 ASN cc_start: 0.7493 (t0) cc_final: 0.7276 (t0)
REVERT: B  212 ASP cc_start: 0.6797 (t70) cc_final: 0.6492 (t0)
REVERT: B  234 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7801 (m-80)
REVERT: B  283 ARG cc_start: 0.7423 (tpp80) cc_final: 0.7161 (tpp80)
REVERT: B  314 ARG cc_start: 0.7408 (ttt90) cc_final: 0.7156 (ttt90)
REVERT: C   15 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7481 (tm)
REVERT: N   12 VAL cc_start: 0.8453 (p) cc_final: 0.8242 (t)
REVERT: N   80 TYR cc_start: 0.7609 (m-80) cc_final: 0.7301 (m-80)
REVERT: R    9 CYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5407 (m)
REVERT: R   52 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.7001 (mp)
REVERT: R  155 HIS cc_start: 0.6581 (m90) cc_final: 0.6276 (m-70)
REVERT: R  169 PHE cc_start: 0.6445 (t80) cc_final: 0.5615 (t80)
REVERT: R  277 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7212 (mt)
  outliers start: 40
  outliers final: 27
  residues processed: 156
  average time/residue: 0.1190
  time to fit residues: 24.2216
Evaluate side-chains
  160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   15 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 74 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0670
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.167282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.150452 restraints weight = 11023.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 1.83
r_work: 0.3877 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3733 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8140  Z= 0.135
  Angle     :  0.544   6.747  11074  Z= 0.291
  Chirality :  0.042   0.259   1254
  Planarity :  0.004   0.064   1425
  Dihedral  :  4.496  46.318   1125
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.65 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.26), residues: 1023
  helix:  1.87 (0.26), residues: 392
  sheet: -0.58 (0.36), residues: 200
  loop : -1.66 (0.27), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 216 
 TYR   0.029   0.002   TYR N 115 
 PHE   0.016   0.002   PHE R 172 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8139)
  covalent geometry    : angle       0.54361 (11072)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.57479 (    2)
  hydrogen bonds       : bond        0.03998 (  392)
  hydrogen bonds       : angle       4.47841 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6503 (mmp-170)
REVERT: A  299 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5215 (pp20)
REVERT: B   61 MET cc_start: 0.8049 (ppp) cc_final: 0.7204 (ppp)
REVERT: B  125 ASN cc_start: 0.7496 (t0) cc_final: 0.7283 (t0)
REVERT: B  212 ASP cc_start: 0.6680 (t70) cc_final: 0.6377 (t0)
REVERT: B  234 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7793 (m-80)
REVERT: B  283 ARG cc_start: 0.7412 (tpp80) cc_final: 0.7203 (tpp80)
REVERT: B  314 ARG cc_start: 0.7444 (ttt90) cc_final: 0.7208 (ttt90)
REVERT: C   15 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7483 (tm)
REVERT: N   80 TYR cc_start: 0.7607 (m-80) cc_final: 0.7304 (m-80)
REVERT: R    9 CYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5425 (m)
REVERT: R  155 HIS cc_start: 0.6571 (m90) cc_final: 0.6283 (m-70)
REVERT: R  169 PHE cc_start: 0.6408 (t80) cc_final: 0.5546 (t80)
REVERT: R  277 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7221 (mt)
  outliers start: 38
  outliers final: 29
  residues processed: 151
  average time/residue: 0.1084
  time to fit residues: 21.4243
Evaluate side-chains
  163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ARG
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   15 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.165213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.148196 restraints weight = 11030.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 1.83
r_work: 0.3847 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8140  Z= 0.208
  Angle     :  0.600   6.779  11074  Z= 0.321
  Chirality :  0.044   0.270   1254
  Planarity :  0.005   0.067   1425
  Dihedral  :  4.642  44.272   1125
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.02 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.26), residues: 1023
  helix:  1.72 (0.26), residues: 385
  sheet: -0.64 (0.37), residues: 195
  loop : -1.66 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 216 
 TYR   0.029   0.002   TYR N 115 
 PHE   0.020   0.002   PHE B 235 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.006   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 8139)
  covalent geometry    : angle       0.60001 (11072)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       0.70616 (    2)
  hydrogen bonds       : bond        0.04376 (  392)
  hydrogen bonds       : angle       4.60854 ( 1122)

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

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

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2046 Ramachandran restraints generated.
    1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 LEU cc_start: 0.8297 (mt) cc_final: 0.7967 (mp)
REVERT: A  299 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5625 (pp20)
REVERT: B   61 MET cc_start: 0.7998 (ppp) cc_final: 0.7251 (ptm)
REVERT: B  125 ASN cc_start: 0.7552 (t0) cc_final: 0.7329 (t0)
REVERT: B  212 ASP cc_start: 0.6851 (t70) cc_final: 0.6544 (t0)
REVERT: B  234 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7825 (m-80)
REVERT: B  283 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7238 (tpp80)
REVERT: B  314 ARG cc_start: 0.7455 (ttt90) cc_final: 0.7216 (ttt90)
REVERT: C   15 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (tm)
REVERT: N   80 TYR cc_start: 0.7605 (m-80) cc_final: 0.7287 (m-80)
REVERT: R   52 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7026 (mp)
REVERT: R  155 HIS cc_start: 0.6654 (m90) cc_final: 0.6335 (m-70)
REVERT: R  277 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7243 (mt)
  outliers start: 38
  outliers final: 30
  residues processed: 155
  average time/residue: 0.1095
  time to fit residues: 22.1954
Evaluate side-chains
  164 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  293 ASN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue    9 CYS
Chi-restraints excluded: chain R residue   15 VAL
Chi-restraints excluded: chain R residue   52 LEU
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  212 VAL
Chi-restraints excluded: chain R residue  264 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 94 optimal weight:    0.4980
   chunk 56 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0270
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.166916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.149956 restraints weight = 10980.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 1.83
r_work: 0.3871 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3727 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8140  Z= 0.147
  Angle     :  0.562   6.730  11074  Z= 0.302
  Chirality :  0.042   0.262   1254
  Planarity :  0.004   0.064   1425
  Dihedral  :  4.567  44.752   1125
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.38 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.26), residues: 1023
  helix:  1.89 (0.27), residues: 385
  sheet: -0.66 (0.36), residues: 200
  loop : -1.63 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 216 
 TYR   0.030   0.002   TYR N 115 
 PHE   0.020   0.002   PHE A 222 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8139)
  covalent geometry    : angle       0.56158 (11072)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.64255 (    2)
  hydrogen bonds       : bond        0.04088 (  392)
  hydrogen bonds       : angle       4.51330 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2321.93 seconds
wall clock time: 40 minutes 35.42 seconds (2435.42 seconds total)