Starting phenix.real_space_refine
on Wed Aug  5 00:31:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jhn_36280/08_2026/8jhn_36280.map"
  }
  resolution = 3.75
  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=   0.035
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      45      5.16       5
     C    4911      2.51       5
     N    1368      2.21       5
     O    1449      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7773
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1489
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 4, 'TRANS': 201}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 144
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 82
    Chain: "B"
      Number of atoms: 2375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2375
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 226
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 133
    Chain: "D"
      Number of atoms: 1869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 1869
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 130}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 277}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 526
          Unresolved non-hydrogen angles: 669
          Unresolved non-hydrogen dihedrals: 444
          Unresolved non-hydrogen chiralities: 51
          Planarities with less than four sites: {'ASP:plan': 10, 'HIS:plan': 2, 'PHE:plan': 20, 'GLU:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 2, 'GLN:plan1': 4, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 289
    Chain: "G"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 376
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "H"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1655
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 95
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "D"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'UR9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.77, per 1000 atoms: 0.23
  Number of scatterers: 7773
  At special positions: 0
  Unit cell: (86.922, 117.652, 132.578, 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      45     16.00
     O    1449      8.00
     N    1368      7.00
     C    4911      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  18 " - pdb=" SG  CYS D 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D 266 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 100 " - pdb=" SG  CYS D 177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  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: 0.62
  Conformation dependent library (CDL) restraints added in 484.9 milliseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      37.1% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.523A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.520A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 212 through 217
      removed outlier: 3.503A  pdb=" N   PHE A 216 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.625A  pdb=" N   ASN A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 4.168A  pdb=" N   ILE A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.532A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'D' and resid 24 through 52
      removed outlier: 3.669A  pdb=" N   LYS D  28 " --> pdb=" O   ASP D  24 " (cutoff:3.500A)
      Proline residue:  D  31  - end of helix
      removed outlier: 4.063A  pdb=" N   LEU D  47 " --> pdb=" O   LEU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 89
      Proline residue:  D  81  - end of helix
    Processing helix  chain 'D' and resid 96 through 131
      removed outlier: 3.571A  pdb=" N   HIS D 131 " --> pdb=" O   PHE D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 160
    Processing helix  chain 'D' and resid 160 through 165
      removed outlier: 3.753A  pdb=" N   LYS D 164 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LYS D 165 " --> pdb=" O   HIS D 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 160 through 165'
    Processing helix  chain 'D' and resid 187 through 218
      removed outlier: 3.574A  pdb=" N   ALA D 191 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE D 197 " --> pdb=" O   PHE D 193 " (cutoff:3.500A)
      Proline residue:  D 200  - end of helix
    Processing helix  chain 'D' and resid 219 through 222
      removed outlier: 3.953A  pdb=" N   ARG D 222 " --> pdb=" O   GLN D 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 219 through 222'
    Processing helix  chain 'D' and resid 223 through 262
      removed outlier: 4.178A  pdb=" N   ALA D 237 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      Proline residue:  D 246  - end of helix
    Processing helix  chain 'D' and resid 268 through 289
      removed outlier: 4.300A  pdb=" N   VAL D 272 " --> pdb=" O   VAL D 268 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE D 282 " --> pdb=" O   ILE D 278 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   THR D 283 " --> pdb=" O   THR D 279 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR D 284 " --> pdb=" O   LEU D 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 290 through 295
      removed outlier: 3.658A  pdb=" N   TYR D 294 " --> pdb=" O   ASP D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 305
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.737A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.510A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.732A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.841A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 4.149A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 9.853A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.704A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.058A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.748A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.800A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.780A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.947A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.877A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13
    Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 171
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.748A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR H 118 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.748A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR H 118 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 142
      removed outlier: 3.578A  pdb=" N   VAL H 155 " --> pdb=" O   ILE H 216 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE H 157 " --> pdb=" O   LEU H 214 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS H 159 " --> pdb=" O   PHE H 212 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE H 212 " --> pdb=" O   CYS H 159 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR H 213 " --> pdb=" O   SER H 206 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 194 through 195
      removed outlier: 3.626A  pdb=" N   TYR H 190 " --> pdb=" O   ASN H 194 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY H 225 " --> pdb=" O   LEU H 245 " (cutoff:3.500A)

    408 hydrogen bonds defined for protein.
    1146 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: 1.56

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1280
        1.31 -     1.44: 2223
        1.44 -     1.57: 4372
        1.57 -     1.69: 0
        1.69 -     1.82: 59
  Bond restraints: 7934
  Sorted by residual:
  bond pdb=" C   ALA D 174 "
       pdb=" N   ASN D 175 "
    ideal  model  delta    sigma   weight residual
    1.329  1.269  0.060 1.38e-02 5.25e+03 1.89e+01
  bond pdb=" C   LEU D 280 "
       pdb=" O   LEU D 280 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.046 1.32e-02 5.74e+03 1.23e+01
  bond pdb=" N   SER D 261 "
       pdb=" CA  SER D 261 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 9.10e-03 1.21e+04 1.13e+01
  bond pdb=" N   THR D 263 "
       pdb=" CA  THR D 263 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.22e-02 6.72e+03 9.07e+00
  bond pdb=" N   GLN D 170 "
       pdb=" CA  GLN D 170 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.27e-02 6.20e+03 8.40e+00
  ... (remaining 7929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 10743
        2.75 -     5.51: 82
        5.51 -     8.26: 19
        8.26 -    11.02: 2
       11.02 -    13.77: 1
  Bond angle restraints: 10847
  Sorted by residual:
  angle pdb=" C   ILE D 169 "
        pdb=" N   GLN D 170 "
        pdb=" CA  GLN D 170 "
      ideal   model   delta    sigma   weight residual
     122.84  114.69    8.15 1.30e+00 5.92e-01 3.93e+01
  angle pdb=" O   ILE D 169 "
        pdb=" C   ILE D 169 "
        pdb=" N   GLN D 170 "
      ideal   model   delta    sigma   weight residual
     123.18  116.56    6.62 1.08e+00 8.57e-01 3.75e+01
  angle pdb=" N   ASN D  17 "
        pdb=" CA  ASN D  17 "
        pdb=" C   ASN D  17 "
      ideal   model   delta    sigma   weight residual
     110.30  101.18    9.12 1.50e+00 4.44e-01 3.70e+01
  angle pdb=" N   PHE D 197 "
        pdb=" CA  PHE D 197 "
        pdb=" C   PHE D 197 "
      ideal   model   delta    sigma   weight residual
     113.55  106.57    6.98 1.26e+00 6.30e-01 3.07e+01
  angle pdb=" N   LEU D 280 "
        pdb=" CA  LEU D 280 "
        pdb=" C   LEU D 280 "
      ideal   model   delta    sigma   weight residual
     112.89  106.04    6.85 1.24e+00 6.50e-01 3.05e+01
  ... (remaining 10842 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 4216
       16.70 -    33.40: 305
       33.40 -    50.10: 69
       50.10 -    66.80: 9
       66.80 -    83.50: 6
  Dihedral angle restraints: 4605
    sinusoidal: 1371
      harmonic: 3234
  Sorted by residual:
  dihedral pdb=" CB  CYS D  19 "
           pdb=" SG  CYS D  19 "
           pdb=" SG  CYS D 266 "
           pdb=" CB  CYS D 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.50  -83.50     1      1.00e+01 1.00e-02 8.51e+01
  dihedral pdb=" CB  CYS H 159 "
           pdb=" SG  CYS H 159 "
           pdb=" SG  CYS H 229 "
           pdb=" CB  CYS H 229 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  139.53  -46.53     1      1.00e+01 1.00e-02 3.00e+01
  dihedral pdb=" CA  ALA D 174 "
           pdb=" C   ALA D 174 "
           pdb=" N   ASN D 175 "
           pdb=" CA  ASN D 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.74   23.26     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 4602 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 862
       0.037 -    0.074: 294
       0.074 -    0.111: 89
       0.111 -    0.148: 24
       0.148 -    0.185: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  PHE D  25 "
            pdb=" N   PHE D  25 "
            pdb=" C   PHE D  25 "
            pdb=" CB  PHE D  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.36e-01
  chirality pdb=" CA  LEU D 258 "
            pdb=" N   LEU D 258 "
            pdb=" C   LEU D 258 "
            pdb=" CB  LEU D 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.93e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1409
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 280 "   -0.020 2.00e-02 2.50e+03   4.17e-02 1.74e+01
        pdb=" C   LEU D 280 "    0.072 2.00e-02 2.50e+03
        pdb=" O   LEU D 280 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   SER D 281 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 169 "    0.016 2.00e-02 2.50e+03   2.97e-02 8.80e+00
        pdb=" C   ILE D 169 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ILE D 169 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLN D 170 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 260 "   -0.013 2.00e-02 2.50e+03   2.71e-02 7.33e+00
        pdb=" C   THR D 260 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR D 260 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER D 261 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1406 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 583
        2.74 -     3.28: 7783
        3.28 -     3.82: 12523
        3.82 -     4.36: 13310
        4.36 -     4.90: 24667
  Nonbonded interactions: 58866
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 333 "
            pdb=" OD2 ASP A 337 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   LEU D  66 "
            pdb=" OH  TYR D 294 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   TYR D 284 "
            pdb=" OG  SER D 287 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR H  91 "
            pdb=" O   LEU H 117 "
     model   vdw
     2.269 3.040
  ... (remaining 58861 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.200
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7939  Z= 0.218
  Angle     :  0.669  13.771  10857  Z= 0.410
  Chirality :  0.044   0.185   1275
  Planarity :  0.004   0.045   1409
  Dihedral  : 12.795  75.311   2498
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  0.75 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.27), residues: 1098
  helix:  2.06 (0.29), residues: 360
  sheet: -0.46 (0.32), residues: 276
  loop : -0.29 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 160 
 TYR   0.010   0.001   TYR H 190 
 PHE   0.010   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.22 ( 7934)
  covalent geometry    : angle       0.66863 /  0.41 (10847)
  SS BOND              : bond        0.00341 /  0.21 (    5)
  SS BOND              : angle       1.19773 /  0.70 (   10)
  hydrogen bonds       : bond        0.19755 / 14.20 (  405)
  hydrogen bonds       : angle       7.08732 /  4.93 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 133
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   53 MET cc_start: 0.5566 (mpp) cc_final: 0.3329 (mtm)
REVERT: A  211 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7376 (mmtp)
REVERT: A  333 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: H  246 GLU cc_start: 0.8276 (mp0) cc_final: 0.7519 (pm20)
  outliers start: 4
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0807
  time to fit residues: 15.1377
Evaluate side-chains
  108 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
B 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.137873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.113567 restraints weight = 14904.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.114275 restraints weight = 12339.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.115809 restraints weight = 10414.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.116054 restraints weight = 7552.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.116307 restraints weight = 7033.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7939  Z= 0.167
  Angle     :  0.559   8.644  10857  Z= 0.300
  Chirality :  0.043   0.147   1275
  Planarity :  0.004   0.046   1409
  Dihedral  :  4.158  47.906   1184
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.09 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.27), residues: 1098
  helix:  2.50 (0.28), residues: 367
  sheet: -0.54 (0.30), residues: 292
  loop : -0.13 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  98 
 TYR   0.016   0.001   TYR H 190 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.020   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.17 ( 7934)
  covalent geometry    : angle       0.55817 /  0.30 (10847)
  SS BOND              : bond        0.00420 /  0.28 (    5)
  SS BOND              : angle       0.93474 /  0.57 (   10)
  hydrogen bonds       : bond        0.03905 /  2.71 (  405)
  hydrogen bonds       : angle       4.97166 /  3.45 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7452 (mmtp)
REVERT: A  295 ASN cc_start: 0.8284 (t0) cc_final: 0.7875 (t0)
REVERT: A  319 ILE cc_start: 0.9077 (mt) cc_final: 0.8820 (mt)
REVERT: A  322 HIS cc_start: 0.6857 (m90) cc_final: 0.6643 (m90)
REVERT: A  333 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7630 (tm-30)
REVERT: A  337 ASP cc_start: 0.8645 (m-30) cc_final: 0.7710 (m-30)
REVERT: H   98 ARG cc_start: 0.8758 (ptm-80) cc_final: 0.8302 (ptm160)
  outliers start: 8
  outliers final: 6
  residues processed: 123
  average time/residue: 0.0759
  time to fit residues: 13.0824
Evaluate side-chains
  106 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain G residue   28 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.8357 > 50:)
   chunk 88 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
A 307 GLN
B  17 GLN
D  86 ASN
D 219 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.138967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.113654 restraints weight = 14846.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.113421 restraints weight = 11396.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.114798 restraints weight = 9807.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.115287 restraints weight = 8052.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.115483 restraints weight = 7196.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7939  Z= 0.143
  Angle     :  0.512   7.842  10857  Z= 0.275
  Chirality :  0.042   0.136   1275
  Planarity :  0.004   0.041   1409
  Dihedral  :  4.043  49.021   1184
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.41 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.27), residues: 1098
  helix:  2.78 (0.28), residues: 368
  sheet: -0.57 (0.30), residues: 291
  loop : -0.15 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 125 
 TYR   0.014   0.001   TYR H 190 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 7934)
  covalent geometry    : angle       0.51203 /  0.27 (10847)
  SS BOND              : bond        0.00350 /  0.23 (    5)
  SS BOND              : angle       0.67985 /  0.43 (   10)
  hydrogen bonds       : bond        0.03556 /  2.47 (  405)
  hydrogen bonds       : angle       4.58344 /  3.19 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7457 (mmtp)
REVERT: A  295 ASN cc_start: 0.8374 (t0) cc_final: 0.7934 (t0)
REVERT: A  319 ILE cc_start: 0.9104 (mt) cc_final: 0.8846 (mt)
REVERT: A  333 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7441 (tm-30)
REVERT: A  337 ASP cc_start: 0.8656 (m-30) cc_final: 0.7624 (m-30)
REVERT: D  103 MET cc_start: 0.8385 (tmm) cc_final: 0.8144 (tmm)
REVERT: D  218 ARG cc_start: 0.8789 (tpp80) cc_final: 0.8499 (tpt-90)
REVERT: D  219 GLN cc_start: 0.8988 (tp40) cc_final: 0.8681 (tp-100)
REVERT: H   98 ARG cc_start: 0.8773 (ptm-80) cc_final: 0.8391 (ptt-90)
REVERT: H  246 GLU cc_start: 0.8224 (mp0) cc_final: 0.7234 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 122
  average time/residue: 0.0661
  time to fit residues: 11.5618
Evaluate side-chains
  112 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.121667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098663 restraints weight = 15191.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.098722 restraints weight = 14403.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099294 restraints weight = 13840.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099536 restraints weight = 12190.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099958 restraints weight = 10259.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7939  Z= 0.140
  Angle     :  0.506   7.348  10857  Z= 0.271
  Chirality :  0.042   0.150   1275
  Planarity :  0.004   0.045   1409
  Dihedral  :  3.967  49.616   1184
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.31 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.27), residues: 1098
  helix:  2.98 (0.27), residues: 362
  sheet: -0.66 (0.30), residues: 291
  loop : -0.19 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 128 
 TYR   0.013   0.001   TYR H 190 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 7934)
  covalent geometry    : angle       0.50539 /  0.27 (10847)
  SS BOND              : bond        0.00348 /  0.23 (    5)
  SS BOND              : angle       0.65509 /  0.41 (   10)
  hydrogen bonds       : bond        0.03403 /  2.35 (  405)
  hydrogen bonds       : angle       4.42516 /  3.10 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7387 (mmtp)
REVERT: A  295 ASN cc_start: 0.8321 (t0) cc_final: 0.7910 (t0)
REVERT: A  303 TYR cc_start: 0.8729 (t80) cc_final: 0.8463 (t80)
REVERT: A  319 ILE cc_start: 0.9099 (mt) cc_final: 0.8833 (mt)
REVERT: A  333 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: A  337 ASP cc_start: 0.8509 (m-30) cc_final: 0.7952 (m-30)
REVERT: H   86 LEU cc_start: 0.8636 (mt) cc_final: 0.8401 (mt)
REVERT: H   98 ARG cc_start: 0.8717 (ptm-80) cc_final: 0.8329 (ptt-90)
  outliers start: 15
  outliers final: 10
  residues processed: 120
  average time/residue: 0.0649
  time to fit residues: 11.1665
Evaluate side-chains
  112 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 73 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   chunk 57 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 78 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
D 219 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.121757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.099899 restraints weight = 15005.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.099800 restraints weight = 14116.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099416 restraints weight = 12678.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.099634 restraints weight = 13619.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.100085 restraints weight = 11625.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   7939  Z= 0.132
  Angle     :  0.524   8.142  10857  Z= 0.278
  Chirality :  0.042   0.146   1275
  Planarity :  0.003   0.036   1409
  Dihedral  :  3.998  49.602   1184
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.39 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.27), residues: 1098
  helix:  2.94 (0.27), residues: 363
  sheet: -0.75 (0.30), residues: 288
  loop : -0.17 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 160 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 7934)
  covalent geometry    : angle       0.51902 /  0.28 (10847)
  SS BOND              : bond        0.00808 /  0.45 (    5)
  SS BOND              : angle       2.43650 /  1.41 (   10)
  hydrogen bonds       : bond        0.03239 /  2.24 (  405)
  hydrogen bonds       : angle       4.31361 /  3.01 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7270 (mmtp)
REVERT: A  295 ASN cc_start: 0.8336 (t0) cc_final: 0.7925 (t0)
REVERT: A  303 TYR cc_start: 0.8714 (t80) cc_final: 0.8503 (t80)
REVERT: A  319 ILE cc_start: 0.9041 (mt) cc_final: 0.8764 (mt)
REVERT: A  333 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: A  337 ASP cc_start: 0.8446 (m-30) cc_final: 0.7973 (m-30)
REVERT: H   98 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.8303 (ptt-90)
REVERT: H  183 GLN cc_start: 0.6905 (tt0) cc_final: 0.6621 (tt0)
REVERT: H  231 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7837 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 114
  average time/residue: 0.0703
  time to fit residues: 11.6425
Evaluate side-chains
  111 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 69 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 79 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.121795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.100277 restraints weight = 15084.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099075 restraints weight = 15510.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099451 restraints weight = 14636.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.099913 restraints weight = 12638.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100320 restraints weight = 11508.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7939  Z= 0.131
  Angle     :  0.507   6.404  10857  Z= 0.271
  Chirality :  0.042   0.145   1275
  Planarity :  0.003   0.037   1409
  Dihedral  :  3.983  49.377   1184
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.69 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.27), residues: 1098
  helix:  3.01 (0.27), residues: 362
  sheet: -0.61 (0.31), residues: 280
  loop : -0.21 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 160 
 TYR   0.012   0.001   TYR H 190 
 PHE   0.014   0.001   PHE H  68 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 7934)
  covalent geometry    : angle       0.50358 /  0.27 (10847)
  SS BOND              : bond        0.00646 /  0.37 (    5)
  SS BOND              : angle       1.99794 /  1.15 (   10)
  hydrogen bonds       : bond        0.03208 /  2.21 (  405)
  hydrogen bonds       : angle       4.28697 /  3.00 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7269 (mmtp)
REVERT: A  295 ASN cc_start: 0.8289 (t0) cc_final: 0.7867 (t0)
REVERT: A  319 ILE cc_start: 0.9039 (mt) cc_final: 0.8749 (mt)
REVERT: A  333 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: A  337 ASP cc_start: 0.8388 (m-30) cc_final: 0.7966 (m-30)
REVERT: H   98 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8310 (ptt-90)
  outliers start: 16
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0599
  time to fit residues: 9.8584
Evaluate side-chains
  114 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0570
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0020
   chunk 57 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.5506

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
B 225 HIS
D 219 GLN
** H 231 GLN ** 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 = 0.3660 r_free = 0.3660 target = 0.122728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102244 restraints weight = 15005.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.100610 restraints weight = 15533.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.100932 restraints weight = 14685.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.101189 restraints weight = 12834.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.101339 restraints weight = 12033.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7939  Z= 0.110
  Angle     :  0.491   7.311  10857  Z= 0.261
  Chirality :  0.041   0.143   1275
  Planarity :  0.003   0.037   1409
  Dihedral  :  3.861  48.625   1184
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.14 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.27), residues: 1098
  helix:  2.91 (0.27), residues: 370
  sheet: -0.53 (0.31), residues: 280
  loop : -0.11 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 160 
 TYR   0.019   0.001   TYR A 303 
 PHE   0.016   0.001   PHE H  68 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.002   0.000   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 7934)
  covalent geometry    : angle       0.48888 /  0.26 (10847)
  SS BOND              : bond        0.00552 /  0.32 (    5)
  SS BOND              : angle       1.66741 /  0.96 (   10)
  hydrogen bonds       : bond        0.03034 /  2.09 (  405)
  hydrogen bonds       : angle       4.15397 /  2.91 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7297 (mmtp)
REVERT: A  295 ASN cc_start: 0.8246 (t0) cc_final: 0.7802 (t0)
REVERT: A  319 ILE cc_start: 0.9038 (mt) cc_final: 0.8727 (mt)
REVERT: A  333 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: A  337 ASP cc_start: 0.8356 (m-30) cc_final: 0.8012 (m-30)
REVERT: D  219 GLN cc_start: 0.8736 (tp40) cc_final: 0.8438 (tp-100)
  outliers start: 15
  outliers final: 11
  residues processed: 123
  average time/residue: 0.0620
  time to fit residues: 10.9576
Evaluate side-chains
  113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0570
   chunk 106 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1504

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
B 110 ASN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.120473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098286 restraints weight = 15080.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.097890 restraints weight = 18619.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099051 restraints weight = 16879.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.099022 restraints weight = 13586.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099225 restraints weight = 12321.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7939  Z= 0.168
  Angle     :  0.563  10.606  10857  Z= 0.295
  Chirality :  0.043   0.148   1275
  Planarity :  0.003   0.037   1409
  Dihedral  :  4.119  48.884   1184
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.29 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.27), residues: 1098
  helix:  2.91 (0.27), residues: 363
  sheet: -0.74 (0.30), residues: 288
  loop : -0.14 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  98 
 TYR   0.015   0.002   TYR H 190 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS H 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 7934)
  covalent geometry    : angle       0.56123 /  0.29 (10847)
  SS BOND              : bond        0.00570 /  0.34 (    5)
  SS BOND              : angle       1.60575 /  0.93 (   10)
  hydrogen bonds       : bond        0.03380 /  2.31 (  405)
  hydrogen bonds       : angle       4.28326 /  3.00 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7329 (mmtp)
REVERT: A  295 ASN cc_start: 0.8228 (t0) cc_final: 0.7742 (t0)
REVERT: A  319 ILE cc_start: 0.9018 (mt) cc_final: 0.8774 (mt)
REVERT: A  333 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: A  337 ASP cc_start: 0.8307 (m-30) cc_final: 0.8014 (m-30)
REVERT: D  103 MET cc_start: 0.8253 (tmm) cc_final: 0.7993 (tmm)
  outliers start: 17
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0535
  time to fit residues: 9.1185
Evaluate side-chains
  113 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0770
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0020
   chunk 61 optimal weight:    0.0970
   chunk 89 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 85 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.2344

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 266 HIS
D 219 GLN
H 231 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.123729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.102325 restraints weight = 15073.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.101377 restraints weight = 14573.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.101728 restraints weight = 14288.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.102025 restraints weight = 12521.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102292 restraints weight = 11446.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7939  Z= 0.102
  Angle     :  0.544   9.480  10857  Z= 0.281
  Chirality :  0.042   0.143   1275
  Planarity :  0.003   0.038   1409
  Dihedral  :  3.894  47.665   1184
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 18.48 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.27), residues: 1098
  helix:  2.93 (0.28), residues: 361
  sheet: -0.58 (0.31), residues: 275
  loop : -0.26 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 125 
 TYR   0.013   0.001   TYR A 303 
 PHE   0.013   0.001   PHE H  68 
 TRP   0.009   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 7934)
  covalent geometry    : angle       0.54278 /  0.28 (10847)
  SS BOND              : bond        0.00492 /  0.29 (    5)
  SS BOND              : angle       1.41585 /  0.81 (   10)
  hydrogen bonds       : bond        0.03008 /  2.05 (  405)
  hydrogen bonds       : angle       4.14696 /  2.92 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7244 (mmtp)
REVERT: A  295 ASN cc_start: 0.8263 (t0) cc_final: 0.7840 (t0)
REVERT: A  319 ILE cc_start: 0.9061 (mt) cc_final: 0.8832 (mt)
REVERT: A  333 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: A  337 ASP cc_start: 0.8368 (m-30) cc_final: 0.8050 (m-30)
  outliers start: 9
  outliers final: 8
  residues processed: 112
  average time/residue: 0.0490
  time to fit residues: 8.2608
Evaluate side-chains
  109 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0970
   chunk 85 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.123010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101563 restraints weight = 14938.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.100405 restraints weight = 14815.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.100817 restraints weight = 14518.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.101158 restraints weight = 12819.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.101415 restraints weight = 11688.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7939  Z= 0.119
  Angle     :  0.533   9.012  10857  Z= 0.280
  Chirality :  0.042   0.145   1275
  Planarity :  0.003   0.037   1409
  Dihedral  :  3.892  47.787   1184
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.08 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.27), residues: 1098
  helix:  2.99 (0.27), residues: 360
  sheet: -0.72 (0.30), residues: 296
  loop : -0.09 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 125 
 TYR   0.011   0.001   TYR A 303 
 PHE   0.011   0.001   PHE H  68 
 TRP   0.010   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 7934)
  covalent geometry    : angle       0.53158 /  0.28 (10847)
  SS BOND              : bond        0.00493 /  0.29 (    5)
  SS BOND              : angle       1.39159 /  0.81 (   10)
  hydrogen bonds       : bond        0.03057 /  2.09 (  405)
  hydrogen bonds       : angle       4.14488 /  2.91 ( 1146)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7255 (mmtp)
REVERT: A  295 ASN cc_start: 0.8237 (t0) cc_final: 0.7762 (t0)
REVERT: A  319 ILE cc_start: 0.9082 (mt) cc_final: 0.8845 (mt)
REVERT: A  333 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7404 (tm-30)
REVERT: A  337 ASP cc_start: 0.8343 (m-30) cc_final: 0.8028 (m-30)
REVERT: D  219 GLN cc_start: 0.8704 (tp40) cc_final: 0.8435 (tp-100)
  outliers start: 9
  outliers final: 8
  residues processed: 106
  average time/residue: 0.0572
  time to fit residues: 9.2168
Evaluate side-chains
  109 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  281 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue    2 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 22 optimal weight:    8.9990
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  22 ASN
B  17 GLN
D 184 HIS
** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.120317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.098129 restraints weight = 15184.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.097328 restraints weight = 19481.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098500 restraints weight = 16130.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098686 restraints weight = 12314.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.098889 restraints weight = 11626.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7939  Z= 0.177
  Angle     :  0.571   8.716  10857  Z= 0.302
  Chirality :  0.043   0.150   1275
  Planarity :  0.003   0.037   1409
  Dihedral  :  4.121  45.308   1184
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.48 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.27), residues: 1098
  helix:  2.96 (0.28), residues: 358
  sheet: -0.89 (0.30), residues: 295
  loop : -0.19 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  98 
 TYR   0.016   0.002   TYR H 190 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 ( 7934)
  covalent geometry    : angle       0.56909 /  0.30 (10847)
  SS BOND              : bond        0.00581 /  0.36 (    5)
  SS BOND              : angle       1.52498 /  0.89 (   10)
  hydrogen bonds       : bond        0.03398 /  2.34 (  405)
  hydrogen bonds       : angle       4.30263 /  3.02 ( 1146)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1212.01 seconds
wall clock time: 21 minutes 33.53 seconds (1293.53 seconds total)