Starting phenix.real_space_refine
on Wed Sep 17 13:46:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j31_61104/09_2025/9j31_61104.map"
  }
  resolution = 3.05
  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=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5713      2.51       5
     N    1556      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 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: 8994
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "D"
      Number of atoms: 1764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1764
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1938
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2232
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 11, 'TRANS': 268}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
  Time building chain proxies: 1.99, per 1000 atoms: 0.22
  Number of scatterers: 8994
  At special positions: 0
  Unit cell: (84.63, 119.97, 126.48, 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      59     16.00
     O    1666      8.00
     N    1556      7.00
     C    5713      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 134 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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: 0.88
  Conformation dependent library (CDL) restraints added in 251.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      38.8% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'D' and resid 91 through 94
      removed outlier: 3.800A  pdb=" N   GLY D  94 " --> pdb=" O   SER D  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 91 through 94'
    Processing helix  chain 'D' and resid 100 through 103
      removed outlier: 3.860A  pdb=" N   LYS D 103 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 103'
    Processing helix  chain 'D' and resid 125 through 129
      removed outlier: 3.827A  pdb=" N   THR D 129 " --> pdb=" O   SER D 126 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 262
      removed outlier: 3.725A  pdb=" N   VAL D 262 " --> pdb=" O   ALA D 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.731A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   GLN A 229 " --> pdb=" O   LYS A 226 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 232 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 261
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 290 through 295
      removed outlier: 4.051A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 336
      removed outlier: 3.849A  pdb=" N   ILE A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   SER A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 374
    Processing helix  chain 'R' and resid 23 through 28
    Processing helix  chain 'R' and resid 29 through 56
      removed outlier: 3.684A  pdb=" N   ILE R  33 " --> pdb=" O   PRO R  29 " (cutoff:3.500A)
      Proline residue:  R  41  - end of helix
    Processing helix  chain 'R' and resid 59 through 88
      removed outlier: 3.868A  pdb=" N   TYR R  63 " --> pdb=" O   GLU R  59 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 100 through 129
      removed outlier: 3.607A  pdb=" N   ILE R 104 " --> pdb=" O   LEU R 100 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   TYR R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   THR R 107 " --> pdb=" O   PHE R 103 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE R 113 " --> pdb=" O   ILE R 109 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE R 119 " --> pdb=" O   PHE R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 138 through 157
    Processing helix  chain 'R' and resid 183 through 196
    Processing helix  chain 'R' and resid 198 through 218
    Processing helix  chain 'R' and resid 223 through 245
    Processing helix  chain 'R' and resid 245 through 262
      removed outlier: 3.506A  pdb=" N   HIS R 249 " --> pdb=" O   PHE R 245 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE R 261 " --> pdb=" O   VAL R 257 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN R 262 " --> pdb=" O   LEU R 258 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 267 through 271
      removed outlier: 3.592A  pdb=" N   ASN R 271 " --> pdb=" O   GLY R 268 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 284
      removed outlier: 3.537A  pdb=" N   ALA R 281 " --> pdb=" O   HIS R 277 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER R 284 " --> pdb=" O   LEU R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 294
      removed outlier: 3.946A  pdb=" N   VAL R 288 " --> pdb=" O   SER R 284 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing helix  chain 'R' and resid 298 through 315
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 3.583A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.381A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.629A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.995A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.582A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.690A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.901A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.510A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 45
      removed outlier: 3.559A  pdb=" N   PHE D 118 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER D 109 " --> pdb=" O   PHE D 118 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 50
      removed outlier: 5.976A  pdb=" N   ARG D  76 " --> pdb=" O   TRP D  85 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   TRP D  85 " --> pdb=" O   ARG D  76 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 197
    Processing sheet with id=AB2, first strand: chain 'D' and resid 223 through 227
      removed outlier: 6.503A  pdb=" N   TRP D 214 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 57 through 58
      removed outlier: 4.189A  pdb=" N   VAL A 217 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   PHE A 239 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ASN A 275 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   VAL A 241 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1293 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: 1.42

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2934
        1.34 -     1.46: 2176
        1.46 -     1.58: 3994
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 9188
  Sorted by residual:
  bond pdb=" C   LEU R  78 "
       pdb=" N   PRO R  79 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.28e-02 6.10e+03 3.06e+00
  bond pdb=" CG  LYS B 301 "
       pdb=" CD  LYS B 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.33e+00
  bond pdb=" CB  LYS B 301 "
       pdb=" CG  LYS B 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.16e+00
  bond pdb=" CB  PRO G  53 "
       pdb=" CG  PRO G  53 "
    ideal  model  delta    sigma   weight residual
    1.492  1.562 -0.070 5.00e-02 4.00e+02 1.94e+00
  bond pdb=" CA  MET R 182 "
       pdb=" C   MET R 182 "
    ideal  model  delta    sigma   weight residual
    1.521  1.536 -0.015 1.14e-02 7.69e+03 1.65e+00
  ... (remaining 9183 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 12236
        2.18 -     4.36: 189
        4.36 -     6.55: 19
        6.55 -     8.73: 2
        8.73 -    10.91: 3
  Bond angle restraints: 12449
  Sorted by residual:
  angle pdb=" CB  LYS B 301 "
        pdb=" CG  LYS B 301 "
        pdb=" CD  LYS B 301 "
      ideal   model   delta    sigma   weight residual
     111.30  121.49  -10.19 2.30e+00 1.89e-01 1.96e+01
  angle pdb=" CB  MET D 131 "
        pdb=" CG  MET D 131 "
        pdb=" SD  MET D 131 "
      ideal   model   delta    sigma   weight residual
     112.70  123.61  -10.91 3.00e+00 1.11e-01 1.32e+01
  angle pdb=" N   ASN R  22 "
        pdb=" CA  ASN R  22 "
        pdb=" C   ASN R  22 "
      ideal   model   delta    sigma   weight residual
     114.75  110.43    4.32 1.26e+00 6.30e-01 1.18e+01
  angle pdb=" N   MET R 182 "
        pdb=" CA  MET R 182 "
        pdb=" C   MET R 182 "
      ideal   model   delta    sigma   weight residual
     114.16  109.18    4.98 1.48e+00 4.57e-01 1.13e+01
  angle pdb=" N   PHE R 162 "
        pdb=" CA  PHE R 162 "
        pdb=" C   PHE R 162 "
      ideal   model   delta    sigma   weight residual
     112.72  108.89    3.83 1.28e+00 6.10e-01 8.94e+00
  ... (remaining 12444 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 4535
       16.91 -    33.82: 690
       33.82 -    50.72: 181
       50.72 -    67.63: 25
       67.63 -    84.54: 14
  Dihedral angle restraints: 5445
    sinusoidal: 2130
      harmonic: 3315
  Sorted by residual:
  dihedral pdb=" CB  CYS R  98 "
           pdb=" SG  CYS R  98 "
           pdb=" SG  CYS R 176 "
           pdb=" CB  CYS R 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.18  -68.18     1      1.00e+01 1.00e-02 6.03e+01
  dihedral pdb=" CB  CYS D  60 "
           pdb=" SG  CYS D  60 "
           pdb=" SG  CYS D 134 "
           pdb=" CB  CYS D 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.99   58.01     1      1.00e+01 1.00e-02 4.51e+01
  dihedral pdb=" CA  GLN R  28 "
           pdb=" C   GLN R  28 "
           pdb=" N   PRO R  29 "
           pdb=" CA  PRO R  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.28   21.72     0      5.00e+00 4.00e-02 1.89e+01
  ... (remaining 5442 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 910
       0.036 -    0.071: 343
       0.071 -    0.107: 102
       0.107 -    0.142: 35
       0.142 -    0.178: 2
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CB  THR R 279 "
            pdb=" CA  THR R 279 "
            pdb=" OG1 THR R 279 "
            pdb=" CG2 THR R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  MET B 188 "
            pdb=" N   MET B 188 "
            pdb=" C   MET B 188 "
            pdb=" CB  MET B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.74e-01
  ... (remaining 1389 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN R  28 "    0.065 5.00e-02 4.00e+02   1.00e-01 1.60e+01
        pdb=" N   PRO R  29 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO R  29 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO R  29 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  52 "   -0.065 5.00e-02 4.00e+02   9.74e-02 1.52e+01
        pdb=" N   PRO G  53 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 215 "    0.011 2.00e-02 2.50e+03   1.88e-02 6.18e+00
        pdb=" CG  PHE A 215 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 215 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 215 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 215 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 215 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 215 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 186
        2.67 -     3.23: 8673
        3.23 -     3.78: 14477
        3.78 -     4.34: 19490
        4.34 -     4.90: 32407
  Nonbonded interactions: 75233
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O   LEU R  38 "
            pdb=" OG1 THR R  42 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLU R 153 "
            pdb=" ND2 ASN R 157 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OD1 ASP D 261 "
            pdb=" OH  TYR D 265 "
     model   vdw
     2.223 3.040
  ... (remaining 75228 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.590
  Find NCS groups from input model:        0.050
  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:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9190  Z= 0.148
  Angle     :  0.658  10.910  12453  Z= 0.363
  Chirality :  0.042   0.178   1392
  Planarity :  0.006   0.100   1587
  Dihedral  : 17.216  84.539   3305
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 28.40 %
    Favored  : 71.40 %
  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:  0.38 (0.26), residues: 1126
  helix:  1.41 (0.26), residues: 392
  sheet:  0.24 (0.32), residues: 263
  loop : -0.68 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 266 
 TYR   0.018   0.002   TYR D 141 
 PHE   0.036   0.002   PHE A 215 
 TRP   0.022   0.002   TRP R  81 
 HIS   0.005   0.001   HIS R 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9188)
  covalent geometry    : angle       0.65841 (12449)
  SS BOND              : bond        0.00509 (    2)
  SS BOND              : angle       0.65166 (    4)
  hydrogen bonds       : bond        0.14020 (  459)
  hydrogen bonds       : angle       6.15942 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   46 ARG cc_start: 0.7023 (mtp-110) cc_final: 0.6742 (mtp180)
REVERT: B  127 LYS cc_start: 0.8352 (mttp) cc_final: 0.8060 (mttp)
REVERT: B  129 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7293 (mmm160)
REVERT: B  212 ASP cc_start: 0.7382 (p0) cc_final: 0.7068 (p0)
REVERT: B  259 GLN cc_start: 0.6902 (mt0) cc_final: 0.6518 (mp10)
REVERT: D  121 MET cc_start: 0.7100 (mtm) cc_final: 0.6846 (mtm)
REVERT: D  228 TYR cc_start: 0.7875 (p90) cc_final: 0.7476 (p90)
REVERT: A  213 HIS cc_start: 0.7121 (t-170) cc_final: 0.6880 (t-170)
REVERT: A  257 LYS cc_start: 0.7050 (tttt) cc_final: 0.6476 (ttmt)
REVERT: A  276 LYS cc_start: 0.7980 (mttm) cc_final: 0.7691 (mttt)
REVERT: A  327 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7001 (mm-30)
REVERT: A  339 ARG cc_start: 0.7481 (mtm180) cc_final: 0.7174 (mmp-170)
REVERT: A  374 TYR cc_start: 0.8420 (m-80) cc_final: 0.8127 (m-80)
REVERT: R  196 LEU cc_start: 0.8348 (mt) cc_final: 0.8132 (mt)
REVERT: R  205 MET cc_start: 0.8267 (ttm) cc_final: 0.7978 (ttt)
REVERT: G   26 ASP cc_start: 0.8390 (m-30) cc_final: 0.7842 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0992
  time to fit residues: 25.3142
Evaluate side-chains
  141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0770
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 206 GLN
R  66 ASN
R 219 ASN
** R 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.194220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.155791 restraints weight = 9683.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.33
r_work: 0.3384 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9190  Z= 0.131
  Angle     :  0.563   6.148  12453  Z= 0.298
  Chirality :  0.043   0.142   1392
  Planarity :  0.005   0.070   1587
  Dihedral  :  4.313  23.522   1250
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.35 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.10 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.69 (0.26), residues: 1126
  helix:  1.73 (0.26), residues: 400
  sheet:  0.45 (0.33), residues: 247
  loop : -0.60 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.018   0.002   TYR A 322 
 PHE   0.017   0.001   PHE R 105 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9188)
  covalent geometry    : angle       0.56299 (12449)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       0.60381 (    4)
  hydrogen bonds       : bond        0.03666 (  459)
  hydrogen bonds       : angle       4.83209 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: B  129 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7706 (mmm160)
REVERT: B  212 ASP cc_start: 0.8080 (p0) cc_final: 0.7704 (p0)
REVERT: B  259 GLN cc_start: 0.7758 (mt0) cc_final: 0.7482 (mp10)
REVERT: D  121 MET cc_start: 0.7514 (mtm) cc_final: 0.7124 (mtm)
REVERT: D  228 TYR cc_start: 0.8070 (p90) cc_final: 0.7786 (p90)
REVERT: A  257 LYS cc_start: 0.8180 (tttt) cc_final: 0.7692 (ttmt)
REVERT: A  339 ARG cc_start: 0.7903 (mtm180) cc_final: 0.7688 (mtm-85)
REVERT: R  196 LEU cc_start: 0.8481 (mt) cc_final: 0.8258 (mt)
REVERT: R  205 MET cc_start: 0.8292 (ttm) cc_final: 0.8066 (ttm)
  outliers start: 36
  outliers final: 21
  residues processed: 170
  average time/residue: 0.1001
  time to fit residues: 23.1858
Evaluate side-chains
  147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  250 VAL
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 109 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  53 GLN
R 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.194045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.148627 restraints weight = 9515.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.90
r_work: 0.3259 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9190  Z= 0.142
  Angle     :  0.543   5.869  12453  Z= 0.288
  Chirality :  0.042   0.140   1392
  Planarity :  0.005   0.061   1587
  Dihedral  :  4.271  25.481   1250
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 26.34 %
    Favored  : 70.47 %
  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:  0.70 (0.26), residues: 1126
  helix:  1.80 (0.26), residues: 400
  sheet:  0.35 (0.32), residues: 253
  loop : -0.61 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.017   0.002   TYR A 374 
 PHE   0.016   0.002   PHE R 105 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9188)
  covalent geometry    : angle       0.54282 (12449)
  SS BOND              : bond        0.00409 (    2)
  SS BOND              : angle       0.72094 (    4)
  hydrogen bonds       : bond        0.03530 (  459)
  hydrogen bonds       : angle       4.65381 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.7894 (mpt180)
REVERT: B  129 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7533 (mmm160)
REVERT: B  171 ILE cc_start: 0.6491 (mm) cc_final: 0.6280 (mm)
REVERT: B  212 ASP cc_start: 0.7962 (p0) cc_final: 0.7432 (p0)
REVERT: B  259 GLN cc_start: 0.7661 (mt0) cc_final: 0.7101 (mp10)
REVERT: D  228 TYR cc_start: 0.7871 (p90) cc_final: 0.7631 (p90)
REVERT: A   25 LYS cc_start: 0.8355 (mptt) cc_final: 0.7735 (mtmt)
REVERT: A  257 LYS cc_start: 0.7872 (tttt) cc_final: 0.7270 (ttmt)
REVERT: A  263 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7467 (ttp-110)
REVERT: A  266 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7752 (mtt-85)
REVERT: A  361 ASP cc_start: 0.8617 (m-30) cc_final: 0.8404 (m-30)
REVERT: R  144 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7556 (mt)
REVERT: R  196 LEU cc_start: 0.8391 (mt) cc_final: 0.8186 (mt)
REVERT: R  259 PHE cc_start: 0.5480 (t80) cc_final: 0.5218 (t80)
  outliers start: 31
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0841
  time to fit residues: 18.2866
Evaluate side-chains
  139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 98 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  28 GLN
R  66 ASN
R 219 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.192538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.135142 restraints weight = 9648.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.12
r_work: 0.3154 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9190  Z= 0.136
  Angle     :  0.530   6.380  12453  Z= 0.279
  Chirality :  0.042   0.143   1392
  Planarity :  0.004   0.058   1587
  Dihedral  :  4.160  22.651   1250
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.35 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.54 %
    Favored  : 70.16 %
  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:  0.69 (0.26), residues: 1126
  helix:  1.90 (0.26), residues: 400
  sheet:  0.25 (0.32), residues: 254
  loop : -0.66 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  19 
 TYR   0.018   0.002   TYR A 374 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9188)
  covalent geometry    : angle       0.52948 (12449)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       0.59975 (    4)
  hydrogen bonds       : bond        0.03393 (  459)
  hydrogen bonds       : angle       4.54053 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B   96 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.7928 (mpt180)
REVERT: B  129 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7574 (mmm160)
REVERT: B  156 GLN cc_start: 0.8366 (mt0) cc_final: 0.8123 (mt0)
REVERT: B  212 ASP cc_start: 0.8033 (p0) cc_final: 0.7463 (p0)
REVERT: B  262 MET cc_start: 0.7905 (ptp) cc_final: 0.7679 (ptp)
REVERT: D  121 MET cc_start: 0.7530 (mtm) cc_final: 0.7311 (mtm)
REVERT: D  131 MET cc_start: 0.7875 (mmm) cc_final: 0.7613 (tpp)
REVERT: A  263 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7532 (ttp-110)
REVERT: R  189 MET cc_start: 0.5670 (mmt) cc_final: 0.5395 (tpp)
REVERT: R  205 MET cc_start: 0.8425 (ttm) cc_final: 0.8154 (ttm)
  outliers start: 32
  outliers final: 26
  residues processed: 149
  average time/residue: 0.0937
  time to fit residues: 19.3124
Evaluate side-chains
  140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  222 THR
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 47 optimal weight:   30.0000
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 ASN
R  66 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.190147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.145054 restraints weight = 9540.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.86
r_work: 0.3261 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9190  Z= 0.140
  Angle     :  0.528   5.836  12453  Z= 0.278
  Chirality :  0.042   0.142   1392
  Planarity :  0.004   0.056   1587
  Dihedral  :  4.140  22.801   1250
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.93 %
    Favored  : 70.16 %
  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:  0.72 (0.25), residues: 1126
  helix:  1.96 (0.25), residues: 400
  sheet:  0.23 (0.32), residues: 248
  loop : -0.63 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.018   0.002   TYR A 374 
 PHE   0.017   0.001   PHE R  27 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.008   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9188)
  covalent geometry    : angle       0.52778 (12449)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       0.64679 (    4)
  hydrogen bonds       : bond        0.03386 (  459)
  hydrogen bonds       : angle       4.54486 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.262 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7746 (tm-30)
REVERT: B   42 ARG cc_start: 0.7334 (mmm160) cc_final: 0.7116 (mmm160)
REVERT: B   96 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8017 (mpt180)
REVERT: B  129 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7601 (mmm160)
REVERT: B  156 GLN cc_start: 0.8389 (mt0) cc_final: 0.8188 (mt0)
REVERT: B  212 ASP cc_start: 0.7967 (p0) cc_final: 0.7374 (p0)
REVERT: B  226 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (mm-30)
REVERT: A   10 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7209 (mttp)
REVERT: A   25 LYS cc_start: 0.8500 (mptt) cc_final: 0.7981 (mtmt)
REVERT: A  263 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.7575 (ttp-110)
REVERT: R  144 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (mt)
REVERT: R  189 MET cc_start: 0.5734 (mmt) cc_final: 0.5506 (tpp)
  outliers start: 38
  outliers final: 28
  residues processed: 155
  average time/residue: 0.0894
  time to fit residues: 19.2458
Evaluate side-chains
  146 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue   93 SER
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0470
   chunk 54 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 109 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.7082

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  66 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.190891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.145765 restraints weight = 9500.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 2.80
r_work: 0.3203 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9190  Z= 0.127
  Angle     :  0.515   5.805  12453  Z= 0.272
  Chirality :  0.042   0.231   1392
  Planarity :  0.004   0.056   1587
  Dihedral  :  4.062  22.405   1250
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.44 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 25.72 %
    Favored  : 70.06 %
  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:  0.74 (0.25), residues: 1126
  helix:  2.01 (0.25), residues: 401
  sheet:  0.13 (0.32), residues: 250
  loop : -0.61 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.018   0.002   TYR A 374 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9188)
  covalent geometry    : angle       0.51545 (12449)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.64453 (    4)
  hydrogen bonds       : bond        0.03280 (  459)
  hydrogen bonds       : angle       4.47313 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: B   42 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7027 (mmm160)
REVERT: B   96 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.7928 (mpt180)
REVERT: B  129 ARG cc_start: 0.7804 (ttt90) cc_final: 0.7412 (mmm160)
REVERT: B  156 GLN cc_start: 0.8339 (mt0) cc_final: 0.8106 (mt0)
REVERT: B  212 ASP cc_start: 0.7967 (p0) cc_final: 0.7292 (p0)
REVERT: B  226 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7919 (mm-30)
REVERT: B  303 ASP cc_start: 0.7768 (p0) cc_final: 0.6876 (m-30)
REVERT: D   90 SER cc_start: 0.8208 (t) cc_final: 0.7775 (p)
REVERT: D  131 MET cc_start: 0.7561 (tpp) cc_final: 0.7177 (tpp)
REVERT: A  263 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.7448 (ttp-110)
REVERT: A  266 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7905 (mtt-85)
REVERT: R  135 LYS cc_start: 0.7615 (ttmt) cc_final: 0.6539 (pttp)
REVERT: R  144 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7583 (mt)
REVERT: R  189 MET cc_start: 0.5526 (mmt) cc_final: 0.5253 (tpp)
REVERT: R  205 MET cc_start: 0.8316 (ttm) cc_final: 0.8065 (ttm)
REVERT: G   13 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6665 (tpt90)
  outliers start: 41
  outliers final: 26
  residues processed: 157
  average time/residue: 0.0957
  time to fit residues: 20.7779
Evaluate side-chains
  142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  353 GLU
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 73 optimal weight:    0.0170
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0370
   chunk 5 optimal weight:    0.0980
   chunk 13 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.195346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151924 restraints weight = 9644.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.78
r_work: 0.3335 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9190  Z= 0.097
  Angle     :  0.488   5.673  12453  Z= 0.258
  Chirality :  0.041   0.191   1392
  Planarity :  0.004   0.055   1587
  Dihedral  :  3.854  20.996   1250
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 26.44 %
    Favored  : 70.47 %
  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:  0.91 (0.26), residues: 1126
  helix:  2.19 (0.25), residues: 402
  sheet:  0.28 (0.33), residues: 244
  loop : -0.58 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.013   0.001   TYR A 322 
 PHE   0.014   0.001   PHE R 105 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 9188)
  covalent geometry    : angle       0.48755 (12449)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       0.71840 (    4)
  hydrogen bonds       : bond        0.02974 (  459)
  hydrogen bonds       : angle       4.27642 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: B   96 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8018 (mpt180)
REVERT: B  129 ARG cc_start: 0.7842 (ttt90) cc_final: 0.7449 (mmm160)
REVERT: B  197 ARG cc_start: 0.8302 (mmt-90) cc_final: 0.7660 (mmt-90)
REVERT: B  212 ASP cc_start: 0.7897 (p0) cc_final: 0.7415 (t0)
REVERT: B  303 ASP cc_start: 0.7635 (p0) cc_final: 0.6905 (m-30)
REVERT: D   90 SER cc_start: 0.8139 (t) cc_final: 0.7812 (p)
REVERT: D  131 MET cc_start: 0.7863 (tpp) cc_final: 0.7487 (tpp)
REVERT: A   25 LYS cc_start: 0.8469 (mptt) cc_final: 0.8002 (mtpt)
REVERT: A  263 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7616 (ttp-110)
REVERT: R   78 LEU cc_start: 0.8492 (tp) cc_final: 0.8033 (mp)
REVERT: R  135 LYS cc_start: 0.7718 (ttmt) cc_final: 0.6783 (pttp)
REVERT: R  189 MET cc_start: 0.5410 (mmt) cc_final: 0.5205 (tpp)
  outliers start: 30
  outliers final: 21
  residues processed: 153
  average time/residue: 0.0885
  time to fit residues: 18.9377
Evaluate side-chains
  140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  118 PHE
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 47 optimal weight:   20.0000
   chunk 41 optimal weight:    0.4980
   chunk 13 optimal weight:    0.1980
   chunk 16 optimal weight:    0.2980
   chunk 103 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  66 ASN
R 157 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.193056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.147546 restraints weight = 9580.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.80
r_work: 0.3295 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9190  Z= 0.118
  Angle     :  0.504   5.699  12453  Z= 0.266
  Chirality :  0.042   0.193   1392
  Planarity :  0.004   0.057   1587
  Dihedral  :  3.880  20.787   1250
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.82 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.78 %
    Favored  : 69.65 %
  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:  0.85 (0.25), residues: 1126
  helix:  2.14 (0.25), residues: 408
  sheet:  0.21 (0.32), residues: 249
  loop : -0.63 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.013   0.001   TYR A 322 
 PHE   0.024   0.001   PHE R 259 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9188)
  covalent geometry    : angle       0.50379 (12449)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       0.70302 (    4)
  hydrogen bonds       : bond        0.03146 (  459)
  hydrogen bonds       : angle       4.29342 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.293 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: B   42 ARG cc_start: 0.7251 (mmm160) cc_final: 0.7034 (mmm160)
REVERT: B   96 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8005 (mpt180)
REVERT: B  129 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7476 (mmm160)
REVERT: B  156 GLN cc_start: 0.8396 (mt0) cc_final: 0.8170 (mt0)
REVERT: B  212 ASP cc_start: 0.7985 (p0) cc_final: 0.7436 (t0)
REVERT: B  226 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: B  303 ASP cc_start: 0.7646 (p0) cc_final: 0.6893 (m-30)
REVERT: D   90 SER cc_start: 0.8143 (t) cc_final: 0.7771 (p)
REVERT: D  131 MET cc_start: 0.7883 (tpp) cc_final: 0.7464 (tpp)
REVERT: A   25 LYS cc_start: 0.8460 (mptt) cc_final: 0.7925 (mtmt)
REVERT: R   66 ASN cc_start: 0.8593 (m110) cc_final: 0.8292 (m-40)
REVERT: R  135 LYS cc_start: 0.7786 (ttmt) cc_final: 0.6896 (pttp)
REVERT: R  161 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7454 (tt)
REVERT: R  189 MET cc_start: 0.5311 (mmt) cc_final: 0.5064 (tpp)
REVERT: R  205 MET cc_start: 0.8324 (ttm) cc_final: 0.8014 (ttm)
REVERT: R  243 LEU cc_start: 0.7286 (mt) cc_final: 0.6667 (pp)
REVERT: G   13 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6799 (tpt90)
  outliers start: 25
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1012
  time to fit residues: 20.0617
Evaluate side-chains
  135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  118 PHE
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 3 optimal weight:    0.0970
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0050
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 102 optimal weight:    9.9990
   overall best weight:    0.5594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.191464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.146656 restraints weight = 9587.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.80
r_work: 0.3295 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9190  Z= 0.116
  Angle     :  0.506   6.371  12453  Z= 0.266
  Chirality :  0.042   0.167   1392
  Planarity :  0.004   0.056   1587
  Dihedral  :  3.885  20.148   1250
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 27.47 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.25), residues: 1126
  helix:  2.20 (0.25), residues: 408
  sheet:  0.20 (0.32), residues: 249
  loop : -0.64 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 263 
 TYR   0.017   0.001   TYR A 374 
 PHE   0.025   0.001   PHE R 259 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9188)
  covalent geometry    : angle       0.50594 (12449)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.72075 (    4)
  hydrogen bonds       : bond        0.03142 (  459)
  hydrogen bonds       : angle       4.26931 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7732 (tm-30)
REVERT: B   42 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7055 (mmm160)
REVERT: B   96 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7926 (mpt180)
REVERT: B  129 ARG cc_start: 0.7777 (ttt90) cc_final: 0.7375 (mmm160)
REVERT: B  212 ASP cc_start: 0.7943 (p0) cc_final: 0.7396 (t0)
REVERT: B  226 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7630 (mm-30)
REVERT: B  303 ASP cc_start: 0.7649 (p0) cc_final: 0.6916 (m-30)
REVERT: D   43 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6893 (t)
REVERT: D   90 SER cc_start: 0.8019 (t) cc_final: 0.7617 (p)
REVERT: D  131 MET cc_start: 0.7711 (tpp) cc_final: 0.7252 (tpp)
REVERT: A   25 LYS cc_start: 0.8335 (mptt) cc_final: 0.7738 (mtmt)
REVERT: A  245 ASP cc_start: 0.7898 (t70) cc_final: 0.7667 (t70)
REVERT: A  263 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7571 (ttp-110)
REVERT: R   66 ASN cc_start: 0.8623 (m110) cc_final: 0.8103 (m-40)
REVERT: R  135 LYS cc_start: 0.7717 (ttmt) cc_final: 0.6757 (pttp)
REVERT: R  189 MET cc_start: 0.5080 (mmt) cc_final: 0.4827 (tpp)
REVERT: R  243 LEU cc_start: 0.7162 (mt) cc_final: 0.6550 (pp)
REVERT: G   13 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6792 (tpt90)
  outliers start: 25
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1033
  time to fit residues: 19.5220
Evaluate side-chains
  134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  118 PHE
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 108 optimal weight:   30.0000
   chunk 92 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 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 = 0.4052 r_free = 0.4052 target = 0.186018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131982 restraints weight = 9597.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.22
r_work: 0.3177 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9190  Z= 0.166
  Angle     :  0.556   6.319  12453  Z= 0.292
  Chirality :  0.043   0.171   1392
  Planarity :  0.004   0.057   1587
  Dihedral  :  4.119  22.620   1250
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 28.19 %
    Favored  : 69.55 %
  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:  0.78 (0.25), residues: 1126
  helix:  2.14 (0.26), residues: 400
  sheet:  0.11 (0.32), residues: 254
  loop : -0.64 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 263 
 TYR   0.015   0.002   TYR A 343 
 PHE   0.028   0.002   PHE R 259 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 9188)
  covalent geometry    : angle       0.55597 (12449)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       0.64658 (    4)
  hydrogen bonds       : bond        0.03501 (  459)
  hydrogen bonds       : angle       4.48412 ( 1293)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B   17 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7529 (tt0)
REVERT: B   96 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8003 (mpt180)
REVERT: B  129 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7606 (mmm160)
REVERT: B  212 ASP cc_start: 0.8187 (p0) cc_final: 0.7573 (t0)
REVERT: B  226 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: B  303 ASP cc_start: 0.7938 (p0) cc_final: 0.7261 (m-30)
REVERT: D  131 MET cc_start: 0.7720 (tpp) cc_final: 0.7221 (tpp)
REVERT: A  245 ASP cc_start: 0.8108 (t70) cc_final: 0.7803 (t70)
REVERT: A  263 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.7689 (ttp-110)
REVERT: R   66 ASN cc_start: 0.8752 (m110) cc_final: 0.8134 (m-40)
REVERT: R  135 LYS cc_start: 0.7735 (ttmt) cc_final: 0.6785 (pttp)
REVERT: R  189 MET cc_start: 0.5223 (mmt) cc_final: 0.4896 (tpp)
REVERT: R  205 MET cc_start: 0.8494 (ttm) cc_final: 0.8198 (ttt)
REVERT: R  243 LEU cc_start: 0.7352 (mt) cc_final: 0.6720 (pp)
REVERT: G   13 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6777 (tpt90)
  outliers start: 22
  outliers final: 20
  residues processed: 129
  average time/residue: 0.1004
  time to fit residues: 17.5799
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  118 PHE
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain R residue   19 VAL
Chi-restraints excluded: chain R residue   77 THR
Chi-restraints excluded: chain R residue   88 HIS
Chi-restraints excluded: chain R residue  109 ILE
Chi-restraints excluded: chain R residue  199 LEU
Chi-restraints excluded: chain G residue   13 ARG
Chi-restraints excluded: chain G residue   41 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 3 optimal weight:    0.0070
   chunk 17 optimal weight:    0.9990
   chunk 90 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.192057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146944 restraints weight = 9463.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.77
r_work: 0.3216 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9190  Z= 0.116
  Angle     :  0.515   6.882  12453  Z= 0.271
  Chirality :  0.042   0.161   1392
  Planarity :  0.004   0.055   1587
  Dihedral  :  3.971  20.733   1250
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.00 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 28.81 %
    Favored  : 69.03 %
  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:  0.81 (0.25), residues: 1126
  helix:  2.10 (0.25), residues: 408
  sheet:  0.15 (0.33), residues: 236
  loop : -0.60 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.014   0.001   TYR A 322 
 PHE   0.032   0.001   PHE D 106 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 340 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9188)
  covalent geometry    : angle       0.51504 (12449)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       0.75876 (    4)
  hydrogen bonds       : bond        0.03188 (  459)
  hydrogen bonds       : angle       4.32134 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2334.29 seconds
wall clock time: 40 minutes 49.89 seconds (2449.89 seconds total)