Starting phenix.real_space_refine
on Sat Jul 26 04:28:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dph_27635/07_2025/8dph_27635_trim.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     Cl      1      4.86       5
     C    5259      2.51       5
     N    1367      2.21       5
     O    1499      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8182
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1933
          Classifications: {'peptide': 264}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 9, 'TRANS': 254}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 171
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 80
    Chain: "B"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1683
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 101
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 88
    Chain: "C"
      Number of atoms: 2479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2479
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 84
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 87
    Chain: "D"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 284
          Classifications: {'peptide': 42}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 39}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "E"
      Number of atoms: 1734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1734
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 69
          Unusual residues: {'CLR': 2, 'T4U': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.90, per 1000 atoms: 0.72
  Number of scatterers: 8182
  At special positions: 0
  Unit cell: (89.18, 120.12, 134.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      56     16.00
     O    1499      8.00
     N    1367      7.00
     C    5259      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 127 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " 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: 2.23
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      38.8% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 80
      removed outlier: 3.501A  pdb=" N   ILE A  65 " --> pdb=" O   VAL A  61 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 106
      removed outlier: 5.035A  pdb=" N   PHE A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   MET A  93 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.555A  pdb=" N   SER A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 111 " --> pdb=" O   MET A 107 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 158
      removed outlier: 4.237A  pdb=" N   SER A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A 158 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 166
      removed outlier: 3.669A  pdb=" N   HIS A 162 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 185
      removed outlier: 3.714A  pdb=" N   ALA A 171 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   VAL A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 194
      removed outlier: 3.933A  pdb=" N   VAL A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 200
      removed outlier: 6.954A  pdb=" N   GLU A 198 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 223
      removed outlier: 4.410A  pdb=" N   ILE A 217 " --> pdb=" O   ASN A 213 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   PHE A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 245
      removed outlier: 3.508A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 337
      removed outlier: 4.270A  pdb=" N   GLU A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA A 309 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   SER A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
      Proline residue:  A 326  - end of helix
      removed outlier: 3.604A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 360
      removed outlier: 3.753A  pdb=" N   VAL A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   TRP A 355 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ILE A 356 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY A 357 " --> pdb=" O   PHE A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 368
    Processing helix  chain 'A' and resid 372 through 383
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.862A  pdb=" N   GLU B  28 " --> pdb=" O   ARG B  24 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.515A  pdb=" N   THR B  48 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.515A  pdb=" N   CYS B  99 " --> pdb=" O   TRP B  96 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 116
      No H-bonds generated for 'chain 'B' and resid 114 through 116'
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 145 through 156
      removed outlier: 3.778A  pdb=" N   LEU B 149 " --> pdb=" O   LYS B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 164 through 170
    Processing helix  chain 'B' and resid 185 through 203
      removed outlier: 3.881A  pdb=" N   ALA B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   SER B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 203 " --> pdb=" O   ASP B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 3.682A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 24
    Processing helix  chain 'C' and resid 29 through 34
      removed outlier: 3.559A  pdb=" N   ILE C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'D' and resid 17 through 24
      removed outlier: 3.642A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.506A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.645A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 3.543A  pdb=" N   PHE B  74 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.771A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA C 328 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU C 318 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   GLY C 330 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.709A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.964A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.839A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.977A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA C 203 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.544A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 4.045A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.839A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.298A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLY E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.787A  pdb=" N   GLY E 213 " --> pdb=" O   LEU E 233 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    394 hydrogen bonds defined for protein.
    1092 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: 3.11

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1315
        1.31 -     1.44: 2288
        1.44 -     1.56: 4667
        1.56 -     1.69: 0
        1.69 -     1.81: 83
  Bond restraints: 8353
  Sorted by residual:
  bond pdb=" C10 T4U A 501 "
       pdb="CL12 T4U A 501 "
    ideal  model  delta    sigma   weight residual
    1.757  1.515  0.242 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" C09 T4U A 501 "
       pdb=" C11 T4U A 501 "
    ideal  model  delta    sigma   weight residual
    1.408  1.280  0.128 2.00e-02 2.50e+03 4.10e+01
  bond pdb=" C03 T4U A 501 "
       pdb=" C10 T4U A 501 "
    ideal  model  delta    sigma   weight residual
    1.383  1.276  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C04 T4U A 501 "
       pdb=" C09 T4U A 501 "
    ideal  model  delta    sigma   weight residual
    1.508  1.414  0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" N   VAL A 156 "
       pdb=" CA  VAL A 156 "
    ideal  model  delta    sigma   weight residual
    1.458  1.517 -0.059 1.29e-02 6.01e+03 2.08e+01
  ... (remaining 8348 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 11251
        2.00 -     3.99: 114
        3.99 -     5.99: 21
        5.99 -     7.98: 2
        7.98 -     9.98: 3
  Bond angle restraints: 11391
  Sorted by residual:
  angle pdb=" O   ALA A 155 "
        pdb=" C   ALA A 155 "
        pdb=" N   VAL A 156 "
      ideal   model   delta    sigma   weight residual
     122.46  116.74    5.72 1.38e+00 5.25e-01 1.72e+01
  angle pdb=" N   PRO A 159 "
        pdb=" CA  PRO A 159 "
        pdb=" C   PRO A 159 "
      ideal   model   delta    sigma   weight residual
     113.57  118.98   -5.41 1.31e+00 5.83e-01 1.71e+01
  angle pdb=" N   TRP A 130 "
        pdb=" CA  TRP A 130 "
        pdb=" C   TRP A 130 "
      ideal   model   delta    sigma   weight residual
     110.97  106.64    4.33 1.09e+00 8.42e-01 1.58e+01
  angle pdb=" CA  TRP A 130 "
        pdb=" CB  TRP A 130 "
        pdb=" CG  TRP A 130 "
      ideal   model   delta    sigma   weight residual
     113.60  120.77   -7.17 1.90e+00 2.77e-01 1.43e+01
  angle pdb=" C   SER A 158 "
        pdb=" N   PRO A 159 "
        pdb=" CA  PRO A 159 "
      ideal   model   delta    sigma   weight residual
     119.19  123.08   -3.89 1.06e+00 8.90e-01 1.35e+01
  ... (remaining 11386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 4792
       17.27 -    34.54: 146
       34.54 -    51.80: 32
       51.80 -    69.07: 5
       69.07 -    86.34: 3
  Dihedral angle restraints: 4978
    sinusoidal: 1816
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CA  ALA E 131 "
           pdb=" C   ALA E 131 "
           pdb=" N   THR E 132 "
           pdb=" CA  THR E 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.40   20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PHE A 223 "
           pdb=" C   PHE A 223 "
           pdb=" N   PHE A 224 "
           pdb=" CA  PHE A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.98  -19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CB  GLU A 161 "
           pdb=" CG  GLU A 161 "
           pdb=" CD  GLU A 161 "
           pdb=" OE1 GLU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.34  -86.34     1      3.00e+01 1.11e-03 9.99e+00
  ... (remaining 4975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1264
       0.089 -    0.178: 84
       0.178 -    0.267: 4
       0.267 -    0.357: 0
       0.357 -    0.446: 1
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CB  VAL A 156 "
            pdb=" CA  VAL A 156 "
            pdb=" CG1 VAL A 156 "
            pdb=" CG2 VAL A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.18   -0.45 2.00e-01 2.50e+01 4.97e+00
  chirality pdb=" CA  PRO A 159 "
            pdb=" N   PRO A 159 "
            pdb=" C   PRO A 159 "
            pdb=" CB  PRO A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  ARG A 157 "
            pdb=" N   ARG A 157 "
            pdb=" C   ARG A 157 "
            pdb=" CB  ARG A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1350 not shown)

  Planarity restraints: 1423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 155 "   -0.019 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   ALA A 155 "    0.062 2.00e-02 2.50e+03
        pdb=" O   ALA A 155 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   VAL A 156 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 T4U A 501 "    0.005 2.00e-02 2.50e+03   1.54e-02 5.32e+00
        pdb=" C03 T4U A 501 "    0.017 2.00e-02 2.50e+03
        pdb=" C04 T4U A 501 "   -0.013 2.00e-02 2.50e+03
        pdb=" C06 T4U A 501 "    0.009 2.00e-02 2.50e+03
        pdb=" C08 T4U A 501 "    0.012 2.00e-02 2.50e+03
        pdb=" C09 T4U A 501 "   -0.011 2.00e-02 2.50e+03
        pdb=" C10 T4U A 501 "    0.019 2.00e-02 2.50e+03
        pdb=" C11 T4U A 501 "   -0.009 2.00e-02 2.50e+03
        pdb="CL12 T4U A 501 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "   -0.023 5.00e-02 4.00e+02   3.56e-02 2.02e+00
        pdb=" N   PRO C 236 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1420 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 154
        2.71 -     3.26: 7606
        3.26 -     3.80: 12043
        3.80 -     4.35: 15220
        4.35 -     4.90: 26835
  Nonbonded interactions: 61858
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OD2 ASP A 151 "
            pdb=" OH  TYR B 243 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C  74 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NH1 ARG B  93 "
            pdb=" OD1 ASP B 124 "
     model   vdw
     2.268 3.120
  ... (remaining 61853 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.242   8355  Z= 0.245
  Angle     :  0.558   9.975  11395  Z= 0.311
  Chirality :  0.045   0.446   1353
  Planarity :  0.003   0.036   1423
  Dihedral  :  9.344  86.338   2926
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  1.71 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1065
  helix:  2.09 (0.30), residues: 328
  sheet:  1.31 (0.30), residues: 293
  loop :  0.28 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 130 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.007   0.001   TYR C 105 
 ARG   0.003   0.000   ARG B 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21830 (  394)
  hydrogen bonds       : angle       6.22533 ( 1092)
  SS BOND              : bond        0.00293 (    2)
  SS BOND              : angle       0.91477 (    4)
  covalent geometry    : bond        0.00464 ( 8353)
  covalent geometry    : angle       0.55777 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 261
  time to evaluate  : 1.459 
Fit side-chains
REVERT: A  153 TYR cc_start: 0.8228 (t80) cc_final: 0.8000 (t80)
REVERT: A  318 PHE cc_start: 0.6966 (m-80) cc_final: 0.6686 (m-80)
REVERT: B  136 THR cc_start: 0.8155 (p) cc_final: 0.7913 (t)
REVERT: B  216 THR cc_start: 0.7833 (p) cc_final: 0.7551 (p)
REVERT: B  219 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6607 (p)
REVERT: B  230 ASP cc_start: 0.7256 (m-30) cc_final: 0.7053 (m-30)
REVERT: C   48 ARG cc_start: 0.7579 (mmt180) cc_final: 0.7270 (mmt-90)
REVERT: C   98 SER cc_start: 0.7962 (p) cc_final: 0.7740 (p)
REVERT: C  100 VAL cc_start: 0.8604 (p) cc_final: 0.8315 (t)
REVERT: C  150 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8088 (mmt180)
REVERT: C  168 LEU cc_start: 0.7997 (tp) cc_final: 0.7757 (tt)
REVERT: C  325 MET cc_start: 0.6588 (mtt) cc_final: 0.6323 (mmm)
REVERT: C  340 ASN cc_start: 0.7330 (t0) cc_final: 0.6931 (t0)
REVERT: E   23 SER cc_start: 0.8307 (m) cc_final: 0.7964 (t)
REVERT: E   98 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7387 (ptt180)
REVERT: E  185 SER cc_start: 0.7835 (t) cc_final: 0.7606 (p)
REVERT: E  190 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7322 (mtm110)
  outliers start: 6
  outliers final: 4
  residues processed: 265
  average time/residue: 0.2173
  time to fit residues: 76.9142
Evaluate side-chains
  213 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 208
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 TRP
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  219 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.0670
   chunk 81 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0670
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
B 131 ASN
B 244 ASN
C  88 ASN
C 110 ASN
C 119 ASN
C 220 GLN
C 230 ASN
E  35 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.130037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113814 restraints weight = 12673.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.01
r_work: 0.3337 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8355  Z= 0.134
  Angle     :  0.554   7.816  11395  Z= 0.296
  Chirality :  0.043   0.215   1353
  Planarity :  0.004   0.044   1423
  Dihedral  :  5.213  47.843   1307
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.13 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1065
  helix:  2.33 (0.29), residues: 338
  sheet:  1.54 (0.31), residues: 278
  loop :  0.17 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 332 
 HIS   0.005   0.001   HIS B 209 
 PHE   0.015   0.002   PHE C 199 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.006   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05153 (  394)
  hydrogen bonds       : angle       4.40718 ( 1092)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       0.68130 (    4)
  covalent geometry    : bond        0.00282 ( 8353)
  covalent geometry    : angle       0.55421 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 216
  time to evaluate  : 1.593 
Fit side-chains
REVERT: A  146 CYS cc_start: 0.7775 (t) cc_final: 0.7484 (m)
REVERT: A  153 TYR cc_start: 0.8460 (t80) cc_final: 0.8228 (t80)
REVERT: B  126 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7990 (pttp)
REVERT: B  136 THR cc_start: 0.8448 (p) cc_final: 0.8176 (t)
REVERT: B  194 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8069 (ttp-110)
REVERT: C   98 SER cc_start: 0.8312 (p) cc_final: 0.7850 (t)
REVERT: C  100 VAL cc_start: 0.8671 (p) cc_final: 0.8421 (t)
REVERT: C  150 ARG cc_start: 0.8524 (mmt-90) cc_final: 0.8248 (mmt-90)
REVERT: C  258 ASP cc_start: 0.6230 (t0) cc_final: 0.5493 (t0)
REVERT: C  325 MET cc_start: 0.7786 (mtt) cc_final: 0.7396 (mmm)
REVERT: E   23 SER cc_start: 0.8405 (m) cc_final: 0.8093 (t)
REVERT: E  103 TYR cc_start: 0.8641 (t80) cc_final: 0.8414 (t80)
REVERT: E  185 SER cc_start: 0.8118 (t) cc_final: 0.7872 (p)
REVERT: E  190 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7785 (mtm110)
  outliers start: 19
  outliers final: 11
  residues processed: 227
  average time/residue: 0.2800
  time to fit residues: 85.2997
Evaluate side-chains
  221 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 210
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain E residue   78 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0980
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 99 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
C  88 ASN
C 110 ASN
C 119 ASN
C 230 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.128378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112270 restraints weight = 12886.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.07
r_work: 0.3305 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8355  Z= 0.144
  Angle     :  0.544   7.595  11395  Z= 0.295
  Chirality :  0.044   0.221   1353
  Planarity :  0.004   0.053   1423
  Dihedral  :  4.946  41.286   1304
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 11.11 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.26), residues: 1065
  helix:  2.42 (0.29), residues: 334
  sheet:  1.55 (0.30), residues: 286
  loop : -0.04 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B 209 
 PHE   0.019   0.002   PHE C 241 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.006   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05228 (  394)
  hydrogen bonds       : angle       4.15715 ( 1092)
  SS BOND              : bond        0.00399 (    2)
  SS BOND              : angle       0.66106 (    4)
  covalent geometry    : bond        0.00322 ( 8353)
  covalent geometry    : angle       0.54396 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  146 CYS cc_start: 0.7992 (t) cc_final: 0.7683 (m)
REVERT: A  153 TYR cc_start: 0.8489 (t80) cc_final: 0.8270 (t80)
REVERT: B  126 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7971 (pttp)
REVERT: B  136 THR cc_start: 0.8571 (p) cc_final: 0.8251 (t)
REVERT: B  194 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8132 (ttp-110)
REVERT: C   48 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7796 (mmt-90)
REVERT: C   98 SER cc_start: 0.8341 (p) cc_final: 0.7955 (t)
REVERT: C  100 VAL cc_start: 0.8710 (p) cc_final: 0.8448 (t)
REVERT: C  258 ASP cc_start: 0.6232 (t0) cc_final: 0.5579 (t0)
REVERT: C  325 MET cc_start: 0.7796 (mtt) cc_final: 0.7576 (mmm)
REVERT: E   23 SER cc_start: 0.8411 (m) cc_final: 0.8081 (t)
REVERT: E   93 MET cc_start: 0.7971 (tpp) cc_final: 0.7365 (tpp)
REVERT: E  185 SER cc_start: 0.8121 (t) cc_final: 0.7853 (p)
REVERT: E  190 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7699 (mtm110)
  outliers start: 26
  outliers final: 22
  residues processed: 229
  average time/residue: 0.2221
  time to fit residues: 67.0702
Evaluate side-chains
  229 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Chi-restraints excluded: chain E residue   96 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 98 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 244 ASN
C  88 ASN
C 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.126911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.111116 restraints weight = 12895.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.99
r_work: 0.3299 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8355  Z= 0.147
  Angle     :  0.545   6.975  11395  Z= 0.295
  Chirality :  0.044   0.219   1353
  Planarity :  0.004   0.059   1423
  Dihedral  :  4.847  37.815   1302
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.09 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1065
  helix:  2.37 (0.29), residues: 337
  sheet:  1.53 (0.30), residues: 284
  loop : -0.18 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  96 
 HIS   0.006   0.001   HIS B 209 
 PHE   0.020   0.002   PHE A 328 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.005   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05135 (  394)
  hydrogen bonds       : angle       4.06376 ( 1092)
  SS BOND              : bond        0.00372 (    2)
  SS BOND              : angle       0.64534 (    4)
  covalent geometry    : bond        0.00330 ( 8353)
  covalent geometry    : angle       0.54461 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6308 (pt) cc_final: 0.6048 (mm)
REVERT: A  146 CYS cc_start: 0.8066 (t) cc_final: 0.7574 (m)
REVERT: A  153 TYR cc_start: 0.8519 (t80) cc_final: 0.8304 (t80)
REVERT: A  165 PHE cc_start: 0.6637 (t80) cc_final: 0.6404 (t80)
REVERT: B  126 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7956 (pttp)
REVERT: B  136 THR cc_start: 0.8551 (p) cc_final: 0.8127 (t)
REVERT: B  194 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8091 (ttp-110)
REVERT: C   48 ARG cc_start: 0.8053 (mmt180) cc_final: 0.7808 (mmt-90)
REVERT: C   79 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (mt)
REVERT: C   98 SER cc_start: 0.8367 (p) cc_final: 0.8019 (t)
REVERT: C  100 VAL cc_start: 0.8683 (p) cc_final: 0.8411 (t)
REVERT: C  227 SER cc_start: 0.8364 (m) cc_final: 0.8139 (t)
REVERT: C  258 ASP cc_start: 0.6257 (t0) cc_final: 0.5577 (t0)
REVERT: E   23 SER cc_start: 0.8413 (m) cc_final: 0.8079 (t)
  outliers start: 25
  outliers final: 22
  residues processed: 218
  average time/residue: 0.2270
  time to fit residues: 65.3460
Evaluate side-chains
  226 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 82 optimal weight:    0.2980
   chunk 107 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0000
   chunk 72 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
B 223 ASN
C  88 ASN
C 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.128931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.113089 restraints weight = 12662.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.03
r_work: 0.3327 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8355  Z= 0.106
  Angle     :  0.498   6.775  11395  Z= 0.266
  Chirality :  0.043   0.219   1353
  Planarity :  0.003   0.049   1423
  Dihedral  :  4.576  37.388   1302
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.68 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.26), residues: 1065
  helix:  2.45 (0.29), residues: 342
  sheet:  1.67 (0.31), residues: 281
  loop : -0.10 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  96 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.025   0.001   PHE A 328 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.004   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  394)
  hydrogen bonds       : angle       3.83062 ( 1092)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       0.64408 (    4)
  covalent geometry    : bond        0.00226 ( 8353)
  covalent geometry    : angle       0.49820 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 208
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6309 (pt) cc_final: 0.6035 (mm)
REVERT: A  153 TYR cc_start: 0.8398 (t80) cc_final: 0.8128 (t80)
REVERT: A  165 PHE cc_start: 0.6668 (t80) cc_final: 0.6463 (t80)
REVERT: B   35 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7789 (mtm180)
REVERT: B  126 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8008 (pttp)
REVERT: B  136 THR cc_start: 0.8572 (p) cc_final: 0.8148 (t)
REVERT: C   48 ARG cc_start: 0.8055 (mmt180) cc_final: 0.7832 (mmt-90)
REVERT: C   61 MET cc_start: 0.8098 (ppp) cc_final: 0.7492 (ppp)
REVERT: C   79 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8054 (mt)
REVERT: C   98 SER cc_start: 0.8366 (p) cc_final: 0.8044 (t)
REVERT: C  100 VAL cc_start: 0.8676 (p) cc_final: 0.8403 (t)
REVERT: C  227 SER cc_start: 0.8298 (m) cc_final: 0.8093 (t)
REVERT: C  258 ASP cc_start: 0.6241 (t0) cc_final: 0.5588 (t0)
REVERT: E   23 SER cc_start: 0.8314 (m) cc_final: 0.7986 (t)
REVERT: E   93 MET cc_start: 0.8018 (tpp) cc_final: 0.7445 (ttt)
  outliers start: 23
  outliers final: 18
  residues processed: 219
  average time/residue: 0.2256
  time to fit residues: 64.9671
Evaluate side-chains
  223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   71 GLU
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 105 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0000
   chunk 45 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
C  75 GLN
C  88 ASN
C 110 ASN
C 119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.112333 restraints weight = 12892.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.97
r_work: 0.3314 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8355  Z= 0.120
  Angle     :  0.510   6.862  11395  Z= 0.274
  Chirality :  0.043   0.220   1353
  Planarity :  0.004   0.052   1423
  Dihedral  :  4.635  37.633   1302
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 13.92 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.26), residues: 1065
  helix:  2.47 (0.28), residues: 346
  sheet:  1.64 (0.30), residues: 281
  loop : -0.17 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.020   0.001   PHE A 328 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.004   0.000   ARG E 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  394)
  hydrogen bonds       : angle       3.80400 ( 1092)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       0.81509 (    4)
  covalent geometry    : bond        0.00265 ( 8353)
  covalent geometry    : angle       0.51021 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 204
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6278 (pt) cc_final: 0.6026 (mm)
REVERT: A  146 CYS cc_start: 0.8009 (t) cc_final: 0.7568 (m)
REVERT: A  153 TYR cc_start: 0.8430 (t80) cc_final: 0.8153 (t80)
REVERT: B  136 THR cc_start: 0.8546 (p) cc_final: 0.8099 (t)
REVERT: C   48 ARG cc_start: 0.8038 (mmt180) cc_final: 0.7813 (mmt-90)
REVERT: C   61 MET cc_start: 0.8153 (ppp) cc_final: 0.7567 (ppp)
REVERT: C   79 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8062 (mt)
REVERT: C   98 SER cc_start: 0.8355 (p) cc_final: 0.8047 (t)
REVERT: C  100 VAL cc_start: 0.8680 (p) cc_final: 0.8410 (t)
REVERT: C  227 SER cc_start: 0.8261 (m) cc_final: 0.8044 (t)
REVERT: C  258 ASP cc_start: 0.6293 (t0) cc_final: 0.5612 (t0)
REVERT: E   23 SER cc_start: 0.8330 (m) cc_final: 0.8003 (t)
REVERT: E   93 MET cc_start: 0.8039 (tpp) cc_final: 0.7560 (ttm)
  outliers start: 28
  outliers final: 23
  residues processed: 217
  average time/residue: 0.2127
  time to fit residues: 60.9219
Evaluate side-chains
  223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0370
   chunk 57 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.1660

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

Flipped N/Q/H residues before XYZ refinement:
A 364 ASN
B 223 ASN
C  75 GLN
C  88 ASN
C 110 ASN
C 119 ASN
C 340 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.124996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.109476 restraints weight = 12813.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.96
r_work: 0.3273 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8355  Z= 0.188
  Angle     :  0.595   7.040  11395  Z= 0.320
  Chirality :  0.045   0.215   1353
  Planarity :  0.004   0.071   1423
  Dihedral  :  5.063  38.847   1302
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 14.04 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.26), residues: 1065
  helix:  2.22 (0.28), residues: 342
  sheet:  1.55 (0.31), residues: 277
  loop : -0.45 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  99 
 HIS   0.006   0.001   HIS B 209 
 PHE   0.020   0.002   PHE A 328 
 TYR   0.013   0.002   TYR C 105 
 ARG   0.007   0.001   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05904 (  394)
  hydrogen bonds       : angle       4.08697 ( 1092)
  SS BOND              : bond        0.00397 (    2)
  SS BOND              : angle       1.27825 (    4)
  covalent geometry    : bond        0.00437 ( 8353)
  covalent geometry    : angle       0.59434 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 204
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6340 (pt) cc_final: 0.6128 (mm)
REVERT: A  146 CYS cc_start: 0.8094 (t) cc_final: 0.7692 (m)
REVERT: A  153 TYR cc_start: 0.8531 (t80) cc_final: 0.8294 (t80)
REVERT: B  194 ARG cc_start: 0.8404 (ttp80) cc_final: 0.7969 (ttp-110)
REVERT: C   48 ARG cc_start: 0.8044 (mmt180) cc_final: 0.7733 (mmt-90)
REVERT: C   61 MET cc_start: 0.8145 (ppp) cc_final: 0.7644 (ppp)
REVERT: C   98 SER cc_start: 0.8430 (p) cc_final: 0.8153 (t)
REVERT: C  100 VAL cc_start: 0.8682 (p) cc_final: 0.8415 (t)
REVERT: C  227 SER cc_start: 0.8224 (m) cc_final: 0.8010 (t)
REVERT: C  258 ASP cc_start: 0.6448 (t0) cc_final: 0.5773 (t0)
REVERT: E   20 LEU cc_start: 0.7913 (mt) cc_final: 0.7591 (mp)
REVERT: E   23 SER cc_start: 0.8420 (m) cc_final: 0.8098 (t)
REVERT: E   88 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.7153 (t)
  outliers start: 29
  outliers final: 22
  residues processed: 217
  average time/residue: 0.2906
  time to fit residues: 83.8525
Evaluate side-chains
  222 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 1.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 105 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0970
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 110 ASN
C 119 ASN
C 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.127078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.111248 restraints weight = 12999.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.04
r_work: 0.3297 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8355  Z= 0.130
  Angle     :  0.534   6.784  11395  Z= 0.286
  Chirality :  0.043   0.218   1353
  Planarity :  0.004   0.054   1423
  Dihedral  :  4.846  38.468   1302
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.02 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.26), residues: 1065
  helix:  2.43 (0.28), residues: 342
  sheet:  1.55 (0.31), residues: 278
  loop : -0.43 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  96 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.018   0.001   PHE A 328 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.008   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04795 (  394)
  hydrogen bonds       : angle       3.89798 ( 1092)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.91560 (    4)
  covalent geometry    : bond        0.00291 ( 8353)
  covalent geometry    : angle       0.53354 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 1.040 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6335 (pt) cc_final: 0.6113 (mm)
REVERT: A  146 CYS cc_start: 0.8017 (t) cc_final: 0.7648 (m)
REVERT: A  153 TYR cc_start: 0.8497 (t80) cc_final: 0.8240 (t80)
REVERT: A  318 PHE cc_start: 0.7337 (m-80) cc_final: 0.7126 (m-80)
REVERT: C   48 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7809 (mmt-90)
REVERT: C   61 MET cc_start: 0.8150 (ppp) cc_final: 0.7599 (ppp)
REVERT: C   98 SER cc_start: 0.8458 (p) cc_final: 0.8184 (t)
REVERT: C  100 VAL cc_start: 0.8657 (p) cc_final: 0.8393 (t)
REVERT: C  258 ASP cc_start: 0.6426 (t0) cc_final: 0.5782 (t0)
REVERT: E   23 SER cc_start: 0.8374 (m) cc_final: 0.8042 (t)
REVERT: E   88 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6997 (t)
REVERT: E   93 MET cc_start: 0.8104 (tpp) cc_final: 0.7607 (ttm)
REVERT: E  127 VAL cc_start: 0.8585 (t) cc_final: 0.8305 (m)
REVERT: E  194 SER cc_start: 0.8709 (p) cc_final: 0.8476 (p)
  outliers start: 22
  outliers final: 21
  residues processed: 216
  average time/residue: 0.3396
  time to fit residues: 99.1970
Evaluate side-chains
  226 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 1.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  101 ASN
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 30 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0980
   chunk 28 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0570
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.113515 restraints weight = 12949.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.04
r_work: 0.3331 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8355  Z= 0.101
  Angle     :  0.505   7.316  11395  Z= 0.265
  Chirality :  0.043   0.219   1353
  Planarity :  0.003   0.045   1423
  Dihedral  :  4.542  37.996   1302
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.75 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1065
  helix:  2.62 (0.28), residues: 342
  sheet:  1.60 (0.31), residues: 283
  loop : -0.29 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  96 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE A 328 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.008   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  394)
  hydrogen bonds       : angle       3.70748 ( 1092)
  SS BOND              : bond        0.00275 (    2)
  SS BOND              : angle       0.76111 (    4)
  covalent geometry    : bond        0.00213 ( 8353)
  covalent geometry    : angle       0.50490 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6305 (pt) cc_final: 0.6057 (mm)
REVERT: A  153 TYR cc_start: 0.8351 (t80) cc_final: 0.8091 (t80)
REVERT: A  327 PHE cc_start: 0.6019 (t80) cc_final: 0.5675 (t80)
REVERT: B   48 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7410 (p)
REVERT: C   48 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7835 (mmt-90)
REVERT: C   61 MET cc_start: 0.8097 (ppp) cc_final: 0.7441 (ppp)
REVERT: C   98 SER cc_start: 0.8485 (p) cc_final: 0.8202 (t)
REVERT: C  100 VAL cc_start: 0.8614 (p) cc_final: 0.8343 (t)
REVERT: C  258 ASP cc_start: 0.6364 (t0) cc_final: 0.5755 (t0)
REVERT: E   93 MET cc_start: 0.8072 (tpp) cc_final: 0.7612 (ttm)
REVERT: E  127 VAL cc_start: 0.8580 (t) cc_final: 0.8303 (m)
REVERT: E  194 SER cc_start: 0.8733 (p) cc_final: 0.8512 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 210
  average time/residue: 0.2216
  time to fit residues: 61.7355
Evaluate side-chains
  217 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 201
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 ASN
C  75 GLN
C 110 ASN
C 119 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.126973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.111174 restraints weight = 12606.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.00
r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8355  Z= 0.146
  Angle     :  0.544   6.868  11395  Z= 0.290
  Chirality :  0.044   0.216   1353
  Planarity :  0.004   0.058   1423
  Dihedral  :  4.756  38.161   1302
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.87 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1065
  helix:  2.57 (0.28), residues: 343
  sheet:  1.52 (0.31), residues: 278
  loop : -0.47 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 324 
 HIS   0.005   0.001   HIS B 209 
 PHE   0.019   0.002   PHE A 137 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.008   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04919 (  394)
  hydrogen bonds       : angle       3.85490 ( 1092)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       0.63431 (    4)
  covalent geometry    : bond        0.00334 ( 8353)
  covalent geometry    : angle       0.54392 (11391)

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

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

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2130 Ramachandran restraints generated.
    1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   63 ILE cc_start: 0.6314 (pt) cc_final: 0.6110 (mm)
REVERT: A  146 CYS cc_start: 0.8012 (t) cc_final: 0.7652 (m)
REVERT: A  153 TYR cc_start: 0.8467 (t80) cc_final: 0.8206 (t80)
REVERT: B   48 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7455 (p)
REVERT: C   61 MET cc_start: 0.8073 (ppp) cc_final: 0.7463 (ppp)
REVERT: C   98 SER cc_start: 0.8484 (p) cc_final: 0.8219 (t)
REVERT: C  100 VAL cc_start: 0.8639 (p) cc_final: 0.8369 (t)
REVERT: C  137 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7515 (mtt90)
REVERT: C  258 ASP cc_start: 0.6467 (t0) cc_final: 0.5820 (t0)
REVERT: E   23 SER cc_start: 0.8333 (m) cc_final: 0.7993 (t)
REVERT: E   88 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.7014 (t)
REVERT: E   93 MET cc_start: 0.8092 (tpp) cc_final: 0.7600 (ttm)
REVERT: E  127 VAL cc_start: 0.8591 (t) cc_final: 0.8324 (m)
  outliers start: 18
  outliers final: 15
  residues processed: 211
  average time/residue: 0.2105
  time to fit residues: 58.9629
Evaluate side-chains
  219 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue   82 HIS
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   88 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    0.2980
   chunk 59 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
C 110 ASN
C 119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.127530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112076 restraints weight = 12820.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.90
r_work: 0.3311 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8355  Z= 0.129
  Angle     :  0.531   7.039  11395  Z= 0.282
  Chirality :  0.043   0.218   1353
  Planarity :  0.004   0.055   1423
  Dihedral  :  4.697  38.046   1302
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.12 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.26), residues: 1065
  helix:  2.57 (0.28), residues: 343
  sheet:  1.50 (0.31), residues: 278
  loop : -0.51 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 324 
 HIS   0.004   0.001   HIS B 209 
 PHE   0.015   0.001   PHE A 328 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.008   0.000   ARG B 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04611 (  394)
  hydrogen bonds       : angle       3.80987 ( 1092)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       0.66335 (    4)
  covalent geometry    : bond        0.00291 ( 8353)
  covalent geometry    : angle       0.53083 (11391)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5531.89 seconds
wall clock time: 99 minutes 22.98 seconds (5962.98 seconds total)