Starting phenix.real_space_refine
on Fri Feb 14 06:22:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rx0_24721/02_2025/7rx0_24721.cif"
  }
  resolution = 3.89
  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=   0.010
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      1      5.21       5
     S      55      5.16       5
     C    6047      2.51       5
     N    1679      2.21       5
     O    1882      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9673
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 2482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2482
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 317}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "G"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 395
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 79}
          Link IDs: {'TRANS': 78}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 79
          Planarities with less than four sites: {'UNK:plan-1': 79}
          Unresolved non-hydrogen planarities: 79
    Chain: "A"
      Number of atoms: 3349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 3349
          Classifications: {'peptide': 428}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 3351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3351
          Classifications: {'peptide': 426}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405}
    Chain: "C"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'G2P': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 5
    residue:
      pdb=" N   VAL C  47 " occ=0.71
      ... (5 atoms not shown)
      pdb=" CG2 VAL C  47 " occ=0.71
    residue:
      pdb=" N   PHE C  86 " occ=0.51
      ... (9 atoms not shown)
      pdb=" CZ  PHE C  86 " occ=0.51
    residue:
      pdb=" N   PHE C  91 " occ=0.63
      ... (9 atoms not shown)
      pdb=" CZ  PHE C  91 " occ=0.63
    residue:
      pdb=" N   LEU C 168 " occ=0.62
      ... (6 atoms not shown)
      pdb=" CD2 LEU C 168 " occ=0.62
    residue:
      pdb=" N   SER C 304 " occ=0.51
      ... (4 atoms not shown)
      pdb=" OG  SER C 304 " occ=0.51
  Time building chain proxies: 5.73, per 1000 atoms: 0.59
  Number of scatterers: 9673
  At special positions: 0
  Unit cell: (81.9, 111.8, 118.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      55     16.00
     P       9     15.00
     Mg      1     11.99
     O    1882      8.00
     N    1679      7.00
     C    6047      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2336

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      50.6% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 26 through 31
    Processing helix  chain 'C' and resid 66 through 82
      removed outlier: 4.949A  pdb=" N   GLN C  76 " --> pdb=" O   GLN C  72 " (cutoff:3.500A)
      Proline residue:  C  77  - end of helix
    Processing helix  chain 'C' and resid 99 through 104
    Processing helix  chain 'C' and resid 118 through 132
    Processing helix  chain 'C' and resid 188 through 201
    Processing helix  chain 'C' and resid 266 through 288
      removed outlier: 3.934A  pdb=" N   GLN C 274 " --> pdb=" O   LYS C 270 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ILE C 275 " --> pdb=" O   GLU C 271 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA C 288 " --> pdb=" O   ASN C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 312
      removed outlier: 4.367A  pdb=" N   ASP C 312 " --> pdb=" O   ARG C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 345
      removed outlier: 3.549A  pdb=" N   ARG C 345 " --> pdb=" O   ASN C 341 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 26
    Processing helix  chain 'G' and resid 50 through 62
    Processing helix  chain 'G' and resid 80 through 92
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 71 through 81
      removed outlier: 4.665A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 4.374A  pdb=" N   GLN A  85 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A  87 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 129
    Processing helix  chain 'A' and resid 147 through 161
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 3.880A  pdb=" N   THR A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.655A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.922A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
      removed outlier: 3.537A  pdb=" N   ILE A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 6.171A  pdb=" N   ALA A 299 " --> pdb=" O   PHE A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 339
      removed outlier: 3.786A  pdb=" N   ARG A 339 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 402
      removed outlier: 3.810A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 390 " --> pdb=" O   GLU A 386 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.983A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 437
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 4.537A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 71 through 81
      removed outlier: 4.122A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 90
      No H-bonds generated for 'chain 'B' and resid 88 through 90'
    Processing helix  chain 'B' and resid 102 through 108
    Processing helix  chain 'B' and resid 111 through 129
      removed outlier: 3.855A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 3.625A  pdb=" N   GLY B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 4.176A  pdb=" N   GLU B 196 " --> pdb=" O   HIS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 215
    Processing helix  chain 'B' and resid 223 through 241
      removed outlier: 3.718A  pdb=" N   LEU B 227 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   CYS B 241 " --> pdb=" O   GLY B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 297
      removed outlier: 3.559A  pdb=" N   ASP B 297 " --> pdb=" O   GLN B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 301
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.980A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
    Processing helix  chain 'B' and resid 384 through 400
      removed outlier: 3.736A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLN B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 411
      removed outlier: 3.958A  pdb=" N   GLU B 411 " --> pdb=" O   TRP B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 437
      removed outlier: 3.896A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASP B 437 " --> pdb=" O   GLN B 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 22
      removed outlier: 3.666A  pdb=" N   VAL C 326 " --> pdb=" O   ARG C  21 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   THR C  89 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   ILE C 323 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   PHE C  91 " --> pdb=" O   ILE C 323 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   CYS C 325 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   TYR C  93 " --> pdb=" O   CYS C 325 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS C 249 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL C  90 " --> pdb=" O   HIS C 249 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL C 251 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER C 246 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LEU C 225 " --> pdb=" O   SER C 246 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 22
      removed outlier: 3.666A  pdb=" N   VAL C 326 " --> pdb=" O   ARG C  21 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   THR C  89 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   ILE C 323 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   PHE C  91 " --> pdb=" O   ILE C 323 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   CYS C 325 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   TYR C  93 " --> pdb=" O   CYS C 325 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS C 249 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL C  90 " --> pdb=" O   HIS C 249 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL C 251 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   SER C 246 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LEU C 225 " --> pdb=" O   SER C 246 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL C 184 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 41
    Processing sheet with id=AA4, first strand: chain 'C' and resid 167 through 170
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.203A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.715A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A 168 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 94
      removed outlier: 8.203A  pdb=" N   ILE A  93 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   PHE A  67 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
      removed outlier: 8.715A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 246 through 248
      removed outlier: 6.492A  pdb=" N   ILE A 355 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 94
      removed outlier: 8.194A  pdb=" N   VAL B  93 " --> pdb=" O   ALA B  65 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   LEU B  67 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   VAL B  68 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   PHE B 135 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU B 137 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   GLN B 133 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   ASN B 167 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 204 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
      removed outlier: 7.672A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 56

    467 hydrogen bonds defined for protein.
    1341 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: 2.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3265
        1.34 -     1.46: 2174
        1.46 -     1.58: 4324
        1.58 -     1.70: 13
        1.70 -     1.81: 89
  Bond restraints: 9865
  Sorted by residual:
  bond pdb=" O3B G2P B 501 "
       pdb=" PG  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.716  1.611  0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" O1A G2P B 501 "
       pdb=" PA  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.507  1.611 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" O1B G2P B 501 "
       pdb=" PB  G2P B 501 "
    ideal  model  delta    sigma   weight residual
    1.510  1.609 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C5  GTP A 501 "
       pdb=" C6  GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.390  1.481 -0.091 2.00e-02 2.50e+03 2.06e+01
  bond pdb=" O3A ANP C1401 "
       pdb=" PB  ANP C1401 "
    ideal  model  delta    sigma   weight residual
    1.700  1.610  0.090 2.00e-02 2.50e+03 2.03e+01
  ... (remaining 9860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 13215
        2.74 -     5.49: 160
        5.49 -     8.23: 21
        8.23 -    10.97: 9
       10.97 -    13.71: 2
  Bond angle restraints: 13407
  Sorted by residual:
  angle pdb=" C   THR C 205 "
        pdb=" CA  THR C 205 "
        pdb=" CB  THR C 205 "
      ideal   model   delta    sigma   weight residual
     110.42  124.13  -13.71 1.99e+00 2.53e-01 4.75e+01
  angle pdb=" C   HIS C 204 "
        pdb=" N   THR C 205 "
        pdb=" CA  THR C 205 "
      ideal   model   delta    sigma   weight residual
     121.54  111.50   10.04 1.91e+00 2.74e-01 2.76e+01
  angle pdb=" N   SER C 215 "
        pdb=" CA  SER C 215 "
        pdb=" C   SER C 215 "
      ideal   model   delta    sigma   weight residual
     110.91  115.77   -4.86 1.17e+00 7.31e-01 1.73e+01
  angle pdb=" PA  G2P B 501 "
        pdb=" C3A G2P B 501 "
        pdb=" PB  G2P B 501 "
      ideal   model   delta    sigma   weight residual
     120.83  109.51   11.32 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" N   THR C 208 "
        pdb=" CA  THR C 208 "
        pdb=" C   THR C 208 "
      ideal   model   delta    sigma   weight residual
     108.96  103.00    5.96 1.59e+00 3.96e-01 1.41e+01
  ... (remaining 13402 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.70: 5774
       33.70 -    67.39: 119
       67.39 -   101.08: 13
      101.08 -   134.78: 2
      134.78 -   168.47: 4
  Dihedral angle restraints: 5912
    sinusoidal: 2282
      harmonic: 3630
  Sorted by residual:
  dihedral pdb=" C   THR C 205 "
           pdb=" N   THR C 205 "
           pdb=" CA  THR C 205 "
           pdb=" CB  THR C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -147.69   25.69     0      2.50e+00 1.60e-01 1.06e+02
  dihedral pdb=" N   THR C 205 "
           pdb=" C   THR C 205 "
           pdb=" CA  THR C 205 "
           pdb=" CB  THR C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  142.70  -19.30     0      2.50e+00 1.60e-01 5.96e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -122.26 -168.47     1      2.00e+01 2.50e-03 4.75e+01
  ... (remaining 5909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.199: 1503
       0.199 -    0.398: 1
       0.398 -    0.597: 0
       0.597 -    0.796: 0
       0.796 -    0.995: 1
  Chirality restraints: 1505
  Sorted by residual:
  chirality pdb=" CA  THR C 205 "
            pdb=" N   THR C 205 "
            pdb=" C   THR C 205 "
            pdb=" CB  THR C 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.53    0.99 2.00e-01 2.50e+01 2.47e+01
  chirality pdb=" CA  HIS C 204 "
            pdb=" N   HIS C 204 "
            pdb=" C   HIS C 204 "
            pdb=" CB  HIS C 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" C3' ANP C1401 "
            pdb=" C2' ANP C1401 "
            pdb=" C4' ANP C1401 "
            pdb=" O3' ANP C1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.54    0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 1502 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 202 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.30e+00
        pdb=" C   ALA C 202 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ALA C 202 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG C 203 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 269 "    0.030 5.00e-02 4.00e+02   4.53e-02 3.28e+00
        pdb=" N   PRO B 270 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  31 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO B  32 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.31: 60
        2.31 -     2.96: 5377
        2.96 -     3.61: 15666
        3.61 -     4.25: 22884
        4.25 -     4.90: 36308
  Nonbonded interactions: 80295
  Sorted by model distance:
  nonbonded pdb=" O   ARG C 203 "
            pdb=" O   GLY C 206 "
     model   vdw
     1.666 3.040
  nonbonded pdb=" O2A G2P B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.777 2.170
  nonbonded pdb=" O2G G2P B 501 "
            pdb="MG    MG B 502 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" OH  TYR C 145 "
            pdb=" NH2 ARG C 203 "
     model   vdw
     1.968 3.120
  nonbonded pdb=" OD1 ASN C 200 "
            pdb=" NH2 ARG C 203 "
     model   vdw
     1.996 3.120
  ... (remaining 80290 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=0.41 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.160
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
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      :  0.006   0.105   9865  Z= 0.415
  Angle     :  0.854  13.713  13407  Z= 0.458
  Chirality :  0.051   0.995   1505
  Planarity :  0.004   0.045   1749
  Dihedral  : 15.605 168.471   3576
  Min Nonbonded Distance : 1.666

Molprobity Statistics.
  All-atom Clashscore : 29.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -2.61 (0.22), residues: 1172
  helix: -1.24 (0.20), residues: 491
  sheet: -1.23 (0.31), residues: 198
  loop : -2.37 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 346 
 HIS   0.008   0.002   HIS C 298 
 PHE   0.016   0.002   PHE C 248 
 TYR   0.013   0.002   TYR B 432 
 ARG   0.006   0.000   ARG C 258 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  119 ILE cc_start: 0.8786 (mt) cc_final: 0.8345 (mm)
REVERT: C  149 TYR cc_start: 0.8704 (t80) cc_final: 0.8442 (t80)
REVERT: C  151 GLU cc_start: 0.9099 (mp0) cc_final: 0.8634 (mp0)
REVERT: C  182 LYS cc_start: 0.8830 (tttp) cc_final: 0.8427 (ttmt)
REVERT: C  218 HIS cc_start: 0.8399 (m-70) cc_final: 0.7744 (m-70)
REVERT: C  225 LEU cc_start: 0.8888 (tp) cc_final: 0.8623 (tp)
REVERT: C  274 GLN cc_start: 0.9144 (mt0) cc_final: 0.8111 (pt0)
REVERT: C  301 TYR cc_start: 0.9198 (m-80) cc_final: 0.8717 (m-80)
REVERT: A   18 ASN cc_start: 0.8886 (m-40) cc_final: 0.8559 (t0)
REVERT: A  116 ASP cc_start: 0.9437 (m-30) cc_final: 0.8869 (p0)
REVERT: A  118 VAL cc_start: 0.9722 (m) cc_final: 0.9413 (p)
REVERT: A  127 ASP cc_start: 0.8830 (m-30) cc_final: 0.8551 (m-30)
REVERT: A  155 GLU cc_start: 0.9357 (tp30) cc_final: 0.8858 (tp30)
REVERT: A  196 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8413 (mm-30)
REVERT: A  216 ASN cc_start: 0.9193 (m-40) cc_final: 0.8719 (m110)
REVERT: A  363 VAL cc_start: 0.9237 (t) cc_final: 0.8895 (p)
REVERT: A  401 LYS cc_start: 0.9489 (tppt) cc_final: 0.9274 (tppt)
REVERT: A  430 LYS cc_start: 0.9453 (tptt) cc_final: 0.8912 (tppt)
REVERT: A  433 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8424 (tm-30)
REVERT: B   26 ASP cc_start: 0.9318 (t0) cc_final: 0.9078 (t70)
REVERT: B   37 HIS cc_start: 0.8802 (m-70) cc_final: 0.8292 (m90)
REVERT: B  108 TYR cc_start: 0.8550 (t80) cc_final: 0.8322 (t80)
REVERT: B  156 LYS cc_start: 0.9458 (mttt) cc_final: 0.9101 (mmpt)
REVERT: B  166 MET cc_start: 0.7478 (mmm) cc_final: 0.7047 (mtm)
REVERT: B  199 ASP cc_start: 0.8421 (m-30) cc_final: 0.7889 (m-30)
REVERT: B  214 PHE cc_start: 0.8809 (t80) cc_final: 0.8581 (t80)
REVERT: B  219 LEU cc_start: 0.8663 (mt) cc_final: 0.8311 (mt)
REVERT: B  306 ASP cc_start: 0.9007 (m-30) cc_final: 0.8696 (t70)
REVERT: B  309 HIS cc_start: 0.9000 (m170) cc_final: 0.8352 (m-70)
REVERT: B  332 MET cc_start: 0.9291 (mmt) cc_final: 0.8944 (mmm)
REVERT: B  373 MET cc_start: 0.8297 (ptp) cc_final: 0.7957 (mtp)
REVERT: B  394 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8677 (tp40)
REVERT: B  413 MET cc_start: 0.9131 (mmm) cc_final: 0.8697 (mmm)
REVERT: B  416 MET cc_start: 0.9093 (mmm) cc_final: 0.8126 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.2590
  time to fit residues: 102.7496
Evaluate side-chains
  212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 93 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 31 optimal weight:   50.0000
   chunk 62 optimal weight:    0.0980
   chunk 49 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 37 optimal weight:   50.0000
   chunk 58 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    5.0188

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
A  18 ASN
A  28 HIS
A  31 GLN
A  35 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 ASN
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  14 ASN
B 426 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.085828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.067414 restraints weight = 34016.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.069755 restraints weight = 17698.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.071308 restraints weight = 11010.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9865  Z= 0.238
  Angle     :  0.739   9.275  13407  Z= 0.368
  Chirality :  0.045   0.208   1505
  Planarity :  0.005   0.082   1749
  Dihedral  : 11.062 151.202   1435
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.86 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -1.08 (0.24), residues: 1172
  helix:  0.19 (0.23), residues: 481
  sheet: -0.83 (0.34), residues: 190
  loop : -1.49 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  21 
 HIS   0.007   0.001   HIS C 204 
 PHE   0.019   0.002   PHE B 262 
 TYR   0.044   0.002   TYR C  71 
 ARG   0.013   0.001   ARG C 154 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 257
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  151 GLU cc_start: 0.9084 (mp0) cc_final: 0.8393 (mp0)
REVERT: C  196 LEU cc_start: 0.9183 (mt) cc_final: 0.8979 (mt)
REVERT: C  205 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7478 (t)
REVERT: C  218 HIS cc_start: 0.8450 (m-70) cc_final: 0.7807 (m-70)
REVERT: C  274 GLN cc_start: 0.9176 (mt0) cc_final: 0.8564 (pp30)
REVERT: C  301 TYR cc_start: 0.9209 (m-80) cc_final: 0.8646 (m-80)
REVERT: C  305 LYS cc_start: 0.9242 (mttp) cc_final: 0.9019 (mtpt)
REVERT: A   86 LEU cc_start: 0.9323 (mt) cc_final: 0.8894 (mt)
REVERT: A  196 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8388 (mm-30)
REVERT: A  216 ASN cc_start: 0.8955 (m-40) cc_final: 0.8697 (m110)
REVERT: A  272 TYR cc_start: 0.8433 (t80) cc_final: 0.8062 (t80)
REVERT: A  302 MET cc_start: 0.8346 (mtt) cc_final: 0.8034 (mtt)
REVERT: A  363 VAL cc_start: 0.9267 (t) cc_final: 0.8943 (p)
REVERT: A  372 GLN cc_start: 0.8928 (mp10) cc_final: 0.8688 (mm-40)
REVERT: A  398 MET cc_start: 0.9112 (mpp) cc_final: 0.8849 (mmp)
REVERT: A  413 MET cc_start: 0.9179 (mmm) cc_final: 0.8951 (mmm)
REVERT: A  430 LYS cc_start: 0.9531 (tptt) cc_final: 0.9137 (tppt)
REVERT: A  433 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8704 (tm-30)
REVERT: A  434 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8458 (mt-10)
REVERT: B   26 ASP cc_start: 0.9237 (t0) cc_final: 0.9017 (t70)
REVERT: B   37 HIS cc_start: 0.8678 (m-70) cc_final: 0.8078 (m90)
REVERT: B   68 VAL cc_start: 0.9333 (p) cc_final: 0.8997 (m)
REVERT: B   69 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7037 (t70)
REVERT: B  107 HIS cc_start: 0.8421 (t70) cc_final: 0.7712 (t70)
REVERT: B  124 LYS cc_start: 0.9489 (tttp) cc_final: 0.9272 (ttmt)
REVERT: B  156 LYS cc_start: 0.9493 (mttt) cc_final: 0.9235 (mmtm)
REVERT: B  166 MET cc_start: 0.7588 (mmm) cc_final: 0.7315 (mtm)
REVERT: B  211 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8927 (t0)
REVERT: B  219 LEU cc_start: 0.8619 (mt) cc_final: 0.8246 (mt)
REVERT: B  302 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8368 (mtt)
REVERT: B  306 ASP cc_start: 0.8963 (m-30) cc_final: 0.8626 (t0)
REVERT: B  309 HIS cc_start: 0.8795 (m170) cc_final: 0.8027 (m-70)
REVERT: B  323 MET cc_start: 0.8056 (mpp) cc_final: 0.6400 (mpp)
REVERT: B  332 MET cc_start: 0.9248 (mmt) cc_final: 0.8882 (mmm)
REVERT: B  373 MET cc_start: 0.8602 (ptp) cc_final: 0.8226 (mtp)
REVERT: B  391 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9242 (mp)
REVERT: B  417 GLU cc_start: 0.8482 (mp0) cc_final: 0.7882 (mp0)
  outliers start: 26
  outliers final: 10
  residues processed: 268
  average time/residue: 0.2266
  time to fit residues: 83.8450
Evaluate side-chains
  221 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 206
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain B residue   69 ASP
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  391 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 32 optimal weight:   50.0000
   chunk 108 optimal weight:   40.0000
   chunk 35 optimal weight:   50.0000
   chunk 73 optimal weight:   20.0000
   chunk 82 optimal weight:    6.9990
   chunk 118 optimal weight:   20.0000
   chunk 77 optimal weight:   30.0000
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 7 optimal weight:   50.0000
   chunk 54 optimal weight:   30.0000
   overall best weight:   15.3996

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
C  76 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 341 ASN
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 HIS
A 329 ASN
A 342 GLN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 394 GLN
B 406 HIS
B 426 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.081146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.063258 restraints weight = 36109.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.065448 restraints weight = 18940.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.066879 restraints weight = 11888.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9865  Z= 0.366
  Angle     :  0.790  12.581  13407  Z= 0.396
  Chirality :  0.045   0.243   1505
  Planarity :  0.005   0.076   1749
  Dihedral  : 10.982 165.849   1435
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 21.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.99 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -1.00 (0.23), residues: 1172
  helix:  0.34 (0.22), residues: 484
  sheet: -1.03 (0.32), residues: 202
  loop : -1.47 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 346 
 HIS   0.011   0.002   HIS A  28 
 PHE   0.015   0.002   PHE C 248 
 TYR   0.027   0.002   TYR C  71 
 ARG   0.008   0.001   ARG C 203 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 206
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   71 TYR cc_start: 0.8903 (t80) cc_final: 0.8388 (t80)
REVERT: C  119 ILE cc_start: 0.8083 (mm) cc_final: 0.7834 (mm)
REVERT: C  145 TYR cc_start: 0.8576 (t80) cc_final: 0.8317 (t80)
REVERT: C  151 GLU cc_start: 0.9007 (mp0) cc_final: 0.8207 (mp0)
REVERT: C  182 LYS cc_start: 0.8933 (tttp) cc_final: 0.8590 (ttmt)
REVERT: C  218 HIS cc_start: 0.8544 (m-70) cc_final: 0.7890 (m-70)
REVERT: C  274 GLN cc_start: 0.9105 (mt0) cc_final: 0.8490 (pp30)
REVERT: C  301 TYR cc_start: 0.9269 (m-80) cc_final: 0.8761 (m-80)
REVERT: C  305 LYS cc_start: 0.9237 (mttp) cc_final: 0.8977 (mtpt)
REVERT: A   86 LEU cc_start: 0.9349 (mt) cc_final: 0.9002 (mt)
REVERT: A  127 ASP cc_start: 0.8866 (m-30) cc_final: 0.8622 (m-30)
REVERT: A  196 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8350 (mm-30)
REVERT: A  272 TYR cc_start: 0.8553 (t80) cc_final: 0.8250 (t80)
REVERT: A  297 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: A  302 MET cc_start: 0.8451 (mtt) cc_final: 0.7970 (mtt)
REVERT: A  363 VAL cc_start: 0.9256 (t) cc_final: 0.8919 (p)
REVERT: A  372 GLN cc_start: 0.8982 (mp10) cc_final: 0.8679 (mm-40)
REVERT: A  401 LYS cc_start: 0.8877 (pttt) cc_final: 0.8166 (pttt)
REVERT: A  433 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: B  156 LYS cc_start: 0.9560 (mttt) cc_final: 0.9248 (mmpt)
REVERT: B  166 MET cc_start: 0.7986 (mmm) cc_final: 0.7496 (mtm)
REVERT: B  219 LEU cc_start: 0.8732 (mt) cc_final: 0.8368 (mt)
REVERT: B  302 MET cc_start: 0.9081 (mmm) cc_final: 0.8423 (mtt)
REVERT: B  306 ASP cc_start: 0.8928 (m-30) cc_final: 0.8694 (m-30)
REVERT: B  309 HIS cc_start: 0.8782 (m170) cc_final: 0.8271 (m90)
REVERT: B  323 MET cc_start: 0.8003 (mpp) cc_final: 0.6596 (mpp)
REVERT: B  332 MET cc_start: 0.9298 (mmt) cc_final: 0.8976 (mmm)
REVERT: B  373 MET cc_start: 0.8604 (ptp) cc_final: 0.8102 (mtp)
REVERT: B  416 MET cc_start: 0.8598 (ptp) cc_final: 0.8269 (ptp)
REVERT: B  417 GLU cc_start: 0.8369 (mp0) cc_final: 0.8120 (mp0)
REVERT: B  419 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.8468 (p)
REVERT: B  422 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8750 (pp20)
  outliers start: 43
  outliers final: 25
  residues processed: 232
  average time/residue: 0.2209
  time to fit residues: 70.7252
Evaluate side-chains
  212 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 185
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  156 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  301 MET
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 111 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 67 optimal weight:    6.9990
   chunk 81 optimal weight:   30.0000
   chunk 93 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 116 optimal weight:   40.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 HIS
A 226 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.082652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.064709 restraints weight = 34775.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.066940 restraints weight = 18216.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.068396 restraints weight = 11414.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9865  Z= 0.240
  Angle     :  0.740  14.500  13407  Z= 0.365
  Chirality :  0.044   0.166   1505
  Planarity :  0.010   0.380   1749
  Dihedral  : 11.343 169.236   1435
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.90 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.59 (0.24), residues: 1172
  helix:  0.72 (0.23), residues: 479
  sheet: -0.76 (0.33), residues: 200
  loop : -1.29 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 346 
 HIS   0.005   0.001   HIS C 298 
 PHE   0.014   0.001   PHE C 333 
 TYR   0.022   0.002   TYR A 224 
 ARG   0.005   0.001   ARG C 154 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 209
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   71 TYR cc_start: 0.9012 (t80) cc_final: 0.8531 (t80)
REVERT: C  119 ILE cc_start: 0.8167 (mm) cc_final: 0.7753 (mm)
REVERT: C  124 MET cc_start: 0.9002 (mmm) cc_final: 0.8687 (mmm)
REVERT: C  151 GLU cc_start: 0.9055 (mp0) cc_final: 0.8316 (mp0)
REVERT: C  166 ILE cc_start: 0.9359 (pp) cc_final: 0.8826 (mt)
REVERT: C  205 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7478 (t)
REVERT: C  218 HIS cc_start: 0.8534 (m-70) cc_final: 0.7821 (m-70)
REVERT: C  274 GLN cc_start: 0.9052 (mt0) cc_final: 0.8447 (pp30)
REVERT: C  301 TYR cc_start: 0.9285 (m-80) cc_final: 0.8764 (m-80)
REVERT: C  305 LYS cc_start: 0.9240 (mttp) cc_final: 0.8903 (mtpt)
REVERT: C  338 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8719 (t0)
REVERT: A   36 MET cc_start: 0.9066 (tmm) cc_final: 0.8856 (tmm)
REVERT: A   86 LEU cc_start: 0.9357 (mt) cc_final: 0.9004 (mt)
REVERT: A  116 ASP cc_start: 0.9125 (p0) cc_final: 0.8635 (p0)
REVERT: A  127 ASP cc_start: 0.8877 (m-30) cc_final: 0.8623 (m-30)
REVERT: A  196 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8429 (mm-30)
REVERT: A  272 TYR cc_start: 0.8541 (t80) cc_final: 0.8144 (t80)
REVERT: A  285 GLN cc_start: 0.2976 (OUTLIER) cc_final: 0.1912 (mt0)
REVERT: A  302 MET cc_start: 0.8514 (mtt) cc_final: 0.8061 (mtt)
REVERT: A  363 VAL cc_start: 0.9230 (t) cc_final: 0.8905 (p)
REVERT: A  372 GLN cc_start: 0.9115 (mp10) cc_final: 0.8853 (mm-40)
REVERT: A  401 LYS cc_start: 0.8892 (pttt) cc_final: 0.8232 (pttt)
REVERT: B  107 HIS cc_start: 0.8416 (t70) cc_final: 0.7735 (t70)
REVERT: B  156 LYS cc_start: 0.9553 (mttt) cc_final: 0.9169 (mmtm)
REVERT: B  159 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: B  166 MET cc_start: 0.8016 (mmm) cc_final: 0.7608 (mtm)
REVERT: B  219 LEU cc_start: 0.8700 (mt) cc_final: 0.8346 (mt)
REVERT: B  269 MET cc_start: 0.8212 (pmm) cc_final: 0.7972 (pmm)
REVERT: B  302 MET cc_start: 0.9088 (mmm) cc_final: 0.8443 (mtt)
REVERT: B  306 ASP cc_start: 0.8936 (m-30) cc_final: 0.8646 (m-30)
REVERT: B  309 HIS cc_start: 0.8738 (m170) cc_final: 0.8197 (m90)
REVERT: B  323 MET cc_start: 0.7994 (mpp) cc_final: 0.6577 (mpp)
REVERT: B  332 MET cc_start: 0.9382 (mmt) cc_final: 0.9003 (mmm)
REVERT: B  346 TRP cc_start: 0.7651 (m100) cc_final: 0.7354 (m100)
REVERT: B  373 MET cc_start: 0.8640 (ptp) cc_final: 0.8144 (mtp)
  outliers start: 40
  outliers final: 23
  residues processed: 233
  average time/residue: 0.2152
  time to fit residues: 70.3658
Evaluate side-chains
  218 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  378 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 33 optimal weight:   60.0000
   chunk 45 optimal weight:    9.9990
   chunk 122 optimal weight:   20.0000
   chunk 44 optimal weight:   40.0000
   chunk 96 optimal weight:    7.9990
   chunk 75 optimal weight:   40.0000
   chunk 8 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   overall best weight:    8.7992

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.082716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.064509 restraints weight = 34863.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066674 restraints weight = 18454.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.068137 restraints weight = 11710.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9865  Z= 0.253
  Angle     :  0.744  13.211  13407  Z= 0.364
  Chirality :  0.044   0.222   1505
  Planarity :  0.004   0.054   1749
  Dihedral  : 10.897 172.782   1435
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 20.40 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.45 (0.24), residues: 1172
  helix:  0.77 (0.23), residues: 482
  sheet: -0.61 (0.33), residues: 195
  loop : -1.18 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 346 
 HIS   0.006   0.001   HIS C 298 
 PHE   0.025   0.002   PHE B 262 
 TYR   0.020   0.002   TYR A 224 
 ARG   0.005   0.001   ARG B 278 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 197
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   71 TYR cc_start: 0.8996 (t80) cc_final: 0.8543 (t80)
REVERT: C  124 MET cc_start: 0.8941 (mmm) cc_final: 0.8645 (mmm)
REVERT: C  149 TYR cc_start: 0.8735 (t80) cc_final: 0.8519 (t80)
REVERT: C  151 GLU cc_start: 0.9091 (mp0) cc_final: 0.8392 (mp0)
REVERT: C  166 ILE cc_start: 0.9386 (pp) cc_final: 0.9165 (tt)
REVERT: C  182 LYS cc_start: 0.8935 (tttp) cc_final: 0.8506 (ttmm)
REVERT: C  205 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7389 (t)
REVERT: C  218 HIS cc_start: 0.8551 (m-70) cc_final: 0.7806 (m-70)
REVERT: C  274 GLN cc_start: 0.9064 (mt0) cc_final: 0.8458 (pp30)
REVERT: C  301 TYR cc_start: 0.9274 (m-80) cc_final: 0.8754 (m-80)
REVERT: C  305 LYS cc_start: 0.9214 (mttp) cc_final: 0.8880 (mtpt)
REVERT: C  338 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8701 (t0)
REVERT: A   21 TRP cc_start: 0.9292 (m100) cc_final: 0.8914 (m100)
REVERT: A   86 LEU cc_start: 0.9365 (mt) cc_final: 0.8985 (mt)
REVERT: A  127 ASP cc_start: 0.8871 (m-30) cc_final: 0.8619 (m-30)
REVERT: A  196 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8424 (mm-30)
REVERT: A  207 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9148 (mm-30)
REVERT: A  272 TYR cc_start: 0.8569 (t80) cc_final: 0.8213 (t80)
REVERT: A  276 ILE cc_start: 0.9553 (tp) cc_final: 0.9337 (tp)
REVERT: A  285 GLN cc_start: 0.3090 (OUTLIER) cc_final: 0.1986 (mt0)
REVERT: A  302 MET cc_start: 0.8453 (mtt) cc_final: 0.8036 (mtt)
REVERT: A  313 MET cc_start: 0.6579 (tpt) cc_final: 0.6094 (tpt)
REVERT: A  363 VAL cc_start: 0.9247 (t) cc_final: 0.8928 (p)
REVERT: A  372 GLN cc_start: 0.9147 (mp10) cc_final: 0.8875 (mm-40)
REVERT: A  377 MET cc_start: 0.8341 (tmm) cc_final: 0.7903 (tmm)
REVERT: A  401 LYS cc_start: 0.8782 (pttt) cc_final: 0.8260 (pttt)
REVERT: A  413 MET cc_start: 0.9176 (mmm) cc_final: 0.8875 (mmp)
REVERT: B  107 HIS cc_start: 0.8394 (t70) cc_final: 0.7748 (t70)
REVERT: B  156 LYS cc_start: 0.9553 (mttt) cc_final: 0.9150 (mmtm)
REVERT: B  159 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7854 (mt-10)
REVERT: B  166 MET cc_start: 0.7905 (mmm) cc_final: 0.7587 (mtm)
REVERT: B  199 ASP cc_start: 0.8696 (m-30) cc_final: 0.7843 (m-30)
REVERT: B  302 MET cc_start: 0.9061 (mmm) cc_final: 0.8575 (mtt)
REVERT: B  309 HIS cc_start: 0.8735 (m170) cc_final: 0.8366 (m90)
REVERT: B  323 MET cc_start: 0.7935 (mpp) cc_final: 0.6274 (mpp)
REVERT: B  332 MET cc_start: 0.9374 (mmt) cc_final: 0.9029 (mmm)
REVERT: B  373 MET cc_start: 0.8579 (ptp) cc_final: 0.8331 (mtp)
  outliers start: 45
  outliers final: 32
  residues processed: 228
  average time/residue: 0.2111
  time to fit residues: 67.1854
Evaluate side-chains
  220 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 185
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  290 GLU
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:   30.0000
   chunk 52 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 81 optimal weight:   40.0000
   chunk 14 optimal weight:   40.0000
   chunk 72 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 87 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN
A 226 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 ASN
** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.083833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.064840 restraints weight = 35284.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.067157 restraints weight = 17794.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.068706 restraints weight = 11056.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9865  Z= 0.208
  Angle     :  0.752  15.704  13407  Z= 0.365
  Chirality :  0.045   0.281   1505
  Planarity :  0.011   0.433   1749
  Dihedral  : 11.129 171.094   1435
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.82 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.33 (0.24), residues: 1172
  helix:  0.89 (0.23), residues: 481
  sheet: -0.60 (0.33), residues: 199
  loop : -1.10 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 346 
 HIS   0.005   0.001   HIS C 298 
 PHE   0.018   0.001   PHE C 250 
 TYR   0.014   0.001   TYR C 149 
 ARG   0.024   0.001   ARG C 203 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 213
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   71 TYR cc_start: 0.8989 (t80) cc_final: 0.8610 (t80)
REVERT: C  102 TYR cc_start: 0.6939 (t80) cc_final: 0.6644 (t80)
REVERT: C  124 MET cc_start: 0.9044 (mmm) cc_final: 0.8774 (mmm)
REVERT: C  151 GLU cc_start: 0.9066 (mp0) cc_final: 0.8608 (mp0)
REVERT: C  205 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7648 (t)
REVERT: C  218 HIS cc_start: 0.8558 (m-70) cc_final: 0.7879 (m-70)
REVERT: C  274 GLN cc_start: 0.8985 (mt0) cc_final: 0.8490 (pm20)
REVERT: C  301 TYR cc_start: 0.9271 (m-80) cc_final: 0.8909 (m-80)
REVERT: C  305 LYS cc_start: 0.9255 (mttp) cc_final: 0.8948 (mtpt)
REVERT: C  338 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8701 (t0)
REVERT: A   86 LEU cc_start: 0.9408 (mt) cc_final: 0.8999 (mt)
REVERT: A  121 ARG cc_start: 0.9255 (mmp80) cc_final: 0.9024 (mmp80)
REVERT: A  127 ASP cc_start: 0.8930 (m-30) cc_final: 0.8666 (m-30)
REVERT: A  196 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8339 (mm-30)
REVERT: A  207 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9277 (mm-30)
REVERT: A  272 TYR cc_start: 0.8536 (t80) cc_final: 0.8185 (t80)
REVERT: A  276 ILE cc_start: 0.9451 (tp) cc_final: 0.9181 (tp)
REVERT: A  302 MET cc_start: 0.8584 (mtt) cc_final: 0.8047 (mtt)
REVERT: A  363 VAL cc_start: 0.9164 (t) cc_final: 0.8818 (p)
REVERT: A  372 GLN cc_start: 0.9160 (mp10) cc_final: 0.8901 (mm-40)
REVERT: A  375 VAL cc_start: 0.9419 (t) cc_final: 0.9109 (p)
REVERT: A  377 MET cc_start: 0.8386 (tmm) cc_final: 0.7811 (tmm)
REVERT: A  380 ASN cc_start: 0.8658 (t0) cc_final: 0.8360 (m-40)
REVERT: A  401 LYS cc_start: 0.8930 (pttt) cc_final: 0.8681 (pttt)
REVERT: A  413 MET cc_start: 0.9213 (mmm) cc_final: 0.8786 (mmm)
REVERT: B  107 HIS cc_start: 0.8669 (t70) cc_final: 0.7923 (t70)
REVERT: B  156 LYS cc_start: 0.9524 (mttt) cc_final: 0.9195 (mmtm)
REVERT: B  159 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: B  166 MET cc_start: 0.8283 (mmm) cc_final: 0.7923 (mtm)
REVERT: B  199 ASP cc_start: 0.8705 (m-30) cc_final: 0.8317 (m-30)
REVERT: B  309 HIS cc_start: 0.8804 (m170) cc_final: 0.8415 (m90)
REVERT: B  323 MET cc_start: 0.7955 (mpp) cc_final: 0.6233 (mpp)
REVERT: B  325 MET cc_start: 0.9005 (mpp) cc_final: 0.8665 (mtm)
REVERT: B  332 MET cc_start: 0.9523 (mmt) cc_final: 0.9126 (mmm)
REVERT: B  345 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8442 (pp20)
REVERT: B  373 MET cc_start: 0.8694 (ptp) cc_final: 0.8298 (mtp)
REVERT: B  413 MET cc_start: 0.8156 (mmt) cc_final: 0.7330 (mmt)
REVERT: B  416 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (ppp)
  outliers start: 42
  outliers final: 30
  residues processed: 239
  average time/residue: 0.2178
  time to fit residues: 72.9787
Evaluate side-chains
  233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 199
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  378 ILE
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 76 optimal weight:   40.0000
   chunk 106 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 12 optimal weight:   30.0000
   chunk 95 optimal weight:   10.0000
   chunk 107 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 112 optimal weight:   30.0000
   overall best weight:    8.3994

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.083081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.064058 restraints weight = 35541.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.066386 restraints weight = 18168.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.067886 restraints weight = 11345.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9865  Z= 0.261
  Angle     :  0.762  14.349  13407  Z= 0.373
  Chirality :  0.044   0.203   1505
  Planarity :  0.004   0.041   1749
  Dihedral  : 10.848 174.222   1435
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 23.03 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.34 (0.24), residues: 1172
  helix:  0.86 (0.23), residues: 479
  sheet: -0.51 (0.33), residues: 200
  loop : -1.13 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP B 346 
 HIS   0.011   0.001   HIS B   6 
 PHE   0.017   0.001   PHE C 250 
 TYR   0.020   0.001   TYR B 224 
 ARG   0.007   0.000   ARG B 278 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 203
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 TYR cc_start: 0.6988 (t80) cc_final: 0.6697 (t80)
REVERT: C  124 MET cc_start: 0.9057 (mmm) cc_final: 0.8847 (mmm)
REVERT: C  151 GLU cc_start: 0.9217 (mp0) cc_final: 0.8613 (mp0)
REVERT: C  182 LYS cc_start: 0.8918 (tttp) cc_final: 0.8515 (tttp)
REVERT: C  205 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7425 (t)
REVERT: C  218 HIS cc_start: 0.8364 (m-70) cc_final: 0.7717 (m-70)
REVERT: C  268 ARG cc_start: 0.9254 (ptt-90) cc_final: 0.8776 (ptt-90)
REVERT: C  274 GLN cc_start: 0.9019 (mt0) cc_final: 0.8474 (pp30)
REVERT: C  301 TYR cc_start: 0.9259 (m-80) cc_final: 0.8891 (m-80)
REVERT: C  305 LYS cc_start: 0.9277 (mttp) cc_final: 0.8975 (mtpt)
REVERT: C  338 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8720 (t0)
REVERT: A   86 LEU cc_start: 0.9405 (mt) cc_final: 0.8972 (mt)
REVERT: A  127 ASP cc_start: 0.8904 (m-30) cc_final: 0.8642 (m-30)
REVERT: A  196 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8345 (mm-30)
REVERT: A  224 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8552 (m-80)
REVERT: A  272 TYR cc_start: 0.8591 (t80) cc_final: 0.8250 (t80)
REVERT: A  276 ILE cc_start: 0.9467 (tp) cc_final: 0.9243 (tp)
REVERT: A  285 GLN cc_start: 0.2793 (OUTLIER) cc_final: 0.1805 (mt0)
REVERT: A  302 MET cc_start: 0.8532 (mtt) cc_final: 0.8051 (mtt)
REVERT: A  363 VAL cc_start: 0.9209 (t) cc_final: 0.8660 (p)
REVERT: A  372 GLN cc_start: 0.9161 (mp10) cc_final: 0.8790 (mm-40)
REVERT: A  375 VAL cc_start: 0.9438 (t) cc_final: 0.9150 (p)
REVERT: A  380 ASN cc_start: 0.8618 (t0) cc_final: 0.8363 (m-40)
REVERT: A  413 MET cc_start: 0.9223 (mmm) cc_final: 0.8839 (mmm)
REVERT: B    8 GLN cc_start: 0.8686 (mt0) cc_final: 0.8163 (mt0)
REVERT: B  107 HIS cc_start: 0.8584 (t70) cc_final: 0.7830 (t70)
REVERT: B  156 LYS cc_start: 0.9550 (mttt) cc_final: 0.9134 (mmtm)
REVERT: B  159 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: B  166 MET cc_start: 0.8139 (mmm) cc_final: 0.7774 (mtm)
REVERT: B  199 ASP cc_start: 0.8669 (m-30) cc_final: 0.8310 (m-30)
REVERT: B  302 MET cc_start: 0.9075 (mmm) cc_final: 0.8344 (mtt)
REVERT: B  309 HIS cc_start: 0.8844 (m170) cc_final: 0.8510 (m90)
REVERT: B  323 MET cc_start: 0.7938 (mpp) cc_final: 0.6548 (mpp)
REVERT: B  332 MET cc_start: 0.9505 (mmt) cc_final: 0.9196 (mmm)
REVERT: B  345 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8307 (pp20)
REVERT: B  400 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7788 (mtt180)
REVERT: B  416 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (ppp)
  outliers start: 47
  outliers final: 31
  residues processed: 233
  average time/residue: 0.2176
  time to fit residues: 70.8815
Evaluate side-chains
  232 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  107 HIS
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 8 optimal weight:   40.0000
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:   50.0000
   chunk 42 optimal weight:   20.0000
   chunk 13 optimal weight:    8.9990
   chunk 55 optimal weight:    0.5980
   chunk 5 optimal weight:    7.9990
   chunk 91 optimal weight:   30.0000
   chunk 46 optimal weight:   30.0000
   chunk 83 optimal weight:   30.0000
   chunk 35 optimal weight:   50.0000
   overall best weight:    8.7190

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

Flipped N/Q/H residues before XYZ refinement:
C  72 GLN
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.082666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063300 restraints weight = 35446.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.065642 restraints weight = 18243.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.067172 restraints weight = 11447.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3442 r_free = 0.3442    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9865  Z= 0.260
  Angle     :  0.810  18.598  13407  Z= 0.398
  Chirality :  0.045   0.313   1505
  Planarity :  0.010   0.396   1749
  Dihedral  : 11.343 175.975   1435
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 24.14 %
    Favored  : 71.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.40 (0.24), residues: 1172
  helix:  0.78 (0.23), residues: 479
  sheet: -0.52 (0.33), residues: 196
  loop : -1.13 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 346 
 HIS   0.012   0.001   HIS B   6 
 PHE   0.024   0.002   PHE A 149 
 TYR   0.036   0.002   TYR C  71 
 ARG   0.018   0.001   ARG C 203 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 203
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 TYR cc_start: 0.7011 (t80) cc_final: 0.6711 (t80)
REVERT: C  149 TYR cc_start: 0.8782 (t80) cc_final: 0.8464 (t80)
REVERT: C  151 GLU cc_start: 0.9077 (mp0) cc_final: 0.8374 (mp0)
REVERT: C  182 LYS cc_start: 0.8949 (tttp) cc_final: 0.8585 (tttp)
REVERT: C  218 HIS cc_start: 0.8477 (m-70) cc_final: 0.7841 (m-70)
REVERT: C  274 GLN cc_start: 0.9013 (mt0) cc_final: 0.8449 (pp30)
REVERT: C  301 TYR cc_start: 0.9231 (m-80) cc_final: 0.8913 (m-80)
REVERT: C  305 LYS cc_start: 0.9241 (mttp) cc_final: 0.8919 (mtpt)
REVERT: C  338 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8715 (t0)
REVERT: A   86 LEU cc_start: 0.9417 (mt) cc_final: 0.8973 (mt)
REVERT: A  124 LYS cc_start: 0.9567 (ttpt) cc_final: 0.9313 (ttpp)
REVERT: A  127 ASP cc_start: 0.8957 (m-30) cc_final: 0.8707 (m-30)
REVERT: A  224 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8498 (m-80)
REVERT: A  272 TYR cc_start: 0.8594 (t80) cc_final: 0.8265 (t80)
REVERT: A  276 ILE cc_start: 0.9451 (tp) cc_final: 0.9231 (tp)
REVERT: A  285 GLN cc_start: 0.2298 (OUTLIER) cc_final: 0.1403 (mt0)
REVERT: A  302 MET cc_start: 0.8538 (mtt) cc_final: 0.8058 (mtt)
REVERT: A  363 VAL cc_start: 0.8877 (t) cc_final: 0.8609 (p)
REVERT: A  372 GLN cc_start: 0.9170 (mp10) cc_final: 0.8798 (mm-40)
REVERT: A  375 VAL cc_start: 0.9426 (t) cc_final: 0.9138 (p)
REVERT: A  377 MET cc_start: 0.8089 (tmm) cc_final: 0.7570 (tmm)
REVERT: A  380 ASN cc_start: 0.8649 (t0) cc_final: 0.8377 (m-40)
REVERT: A  413 MET cc_start: 0.9269 (mmm) cc_final: 0.8924 (mmm)
REVERT: B    8 GLN cc_start: 0.8730 (mt0) cc_final: 0.8156 (mt0)
REVERT: B  156 LYS cc_start: 0.9544 (mttt) cc_final: 0.9160 (mmtm)
REVERT: B  159 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7998 (mt-10)
REVERT: B  166 MET cc_start: 0.8158 (mmm) cc_final: 0.7592 (mtm)
REVERT: B  302 MET cc_start: 0.9102 (mmm) cc_final: 0.8299 (mtt)
REVERT: B  309 HIS cc_start: 0.8880 (m170) cc_final: 0.8543 (m90)
REVERT: B  322 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8668 (mmm160)
REVERT: B  323 MET cc_start: 0.9051 (mpp) cc_final: 0.8737 (mpp)
REVERT: B  332 MET cc_start: 0.9518 (mmt) cc_final: 0.9271 (mmm)
REVERT: B  345 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8148 (pp20)
REVERT: B  346 TRP cc_start: 0.7258 (m100) cc_final: 0.6995 (m100)
REVERT: B  400 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7766 (mtt180)
REVERT: B  416 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (ppp)
  outliers start: 43
  outliers final: 30
  residues processed: 230
  average time/residue: 0.2228
  time to fit residues: 71.7879
Evaluate side-chains
  232 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 197
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  285 GLN
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  398 MET
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 15 optimal weight:   40.0000
   chunk 122 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 108 optimal weight:   30.0000
   chunk 80 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.083498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.064329 restraints weight = 34546.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.066689 restraints weight = 17811.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.068266 restraints weight = 11170.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   9865  Z= 0.250
  Angle     :  0.868  16.586  13407  Z= 0.426
  Chirality :  0.047   0.388   1505
  Planarity :  0.005   0.064   1749
  Dihedral  : 10.954 174.936   1435
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.85 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.35 (0.24), residues: 1172
  helix:  0.80 (0.23), residues: 479
  sheet: -0.52 (0.33), residues: 201
  loop : -1.08 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 346 
 HIS   0.010   0.001   HIS C 204 
 PHE   0.016   0.001   PHE B 272 
 TYR   0.017   0.001   TYR C 145 
 ARG   0.045   0.001   ARG C 203 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 TYR cc_start: 0.6977 (t80) cc_final: 0.6673 (t80)
REVERT: C  149 TYR cc_start: 0.8769 (t80) cc_final: 0.8374 (t80)
REVERT: C  151 GLU cc_start: 0.9045 (mp0) cc_final: 0.8388 (mp0)
REVERT: C  182 LYS cc_start: 0.8923 (tttp) cc_final: 0.8553 (tttp)
REVERT: C  193 LEU cc_start: 0.9216 (tp) cc_final: 0.8948 (pp)
REVERT: C  218 HIS cc_start: 0.8498 (m-70) cc_final: 0.7822 (m-70)
REVERT: C  274 GLN cc_start: 0.8992 (mt0) cc_final: 0.8433 (pp30)
REVERT: C  301 TYR cc_start: 0.9213 (m-80) cc_final: 0.8898 (m-80)
REVERT: C  305 LYS cc_start: 0.9254 (mttp) cc_final: 0.8931 (mtpt)
REVERT: C  338 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8739 (t0)
REVERT: A   86 LEU cc_start: 0.9426 (mt) cc_final: 0.8989 (mt)
REVERT: A  124 LYS cc_start: 0.9566 (ttpt) cc_final: 0.9359 (ttpt)
REVERT: A  127 ASP cc_start: 0.8922 (m-30) cc_final: 0.8651 (m-30)
REVERT: A  224 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8289 (m-80)
REVERT: A  272 TYR cc_start: 0.8545 (t80) cc_final: 0.8176 (t80)
REVERT: A  276 ILE cc_start: 0.9434 (tp) cc_final: 0.9215 (tp)
REVERT: A  302 MET cc_start: 0.8557 (mtt) cc_final: 0.8050 (mtt)
REVERT: A  363 VAL cc_start: 0.8888 (t) cc_final: 0.8607 (p)
REVERT: A  372 GLN cc_start: 0.9167 (mp10) cc_final: 0.8784 (mm-40)
REVERT: A  375 VAL cc_start: 0.9403 (t) cc_final: 0.9104 (p)
REVERT: A  377 MET cc_start: 0.8070 (tmm) cc_final: 0.7564 (tmm)
REVERT: A  380 ASN cc_start: 0.8668 (t0) cc_final: 0.8194 (m-40)
REVERT: A  413 MET cc_start: 0.9225 (mmm) cc_final: 0.8846 (mmm)
REVERT: B    8 GLN cc_start: 0.8792 (mt0) cc_final: 0.8304 (mt0)
REVERT: B  156 LYS cc_start: 0.9536 (mttt) cc_final: 0.9322 (mmtm)
REVERT: B  159 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8002 (mt-10)
REVERT: B  166 MET cc_start: 0.8154 (mmm) cc_final: 0.7592 (mtm)
REVERT: B  235 MET cc_start: 0.8771 (mmt) cc_final: 0.8549 (mmt)
REVERT: B  302 MET cc_start: 0.8966 (mmm) cc_final: 0.8270 (mtt)
REVERT: B  309 HIS cc_start: 0.8858 (m170) cc_final: 0.8588 (m-70)
REVERT: B  322 ARG cc_start: 0.9060 (mmm160) cc_final: 0.8708 (mmm160)
REVERT: B  323 MET cc_start: 0.8787 (mpp) cc_final: 0.7971 (mpp)
REVERT: B  325 MET cc_start: 0.8878 (mpp) cc_final: 0.8140 (mpp)
REVERT: B  332 MET cc_start: 0.9513 (mmt) cc_final: 0.9266 (mmm)
REVERT: B  345 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (pp20)
REVERT: B  373 MET cc_start: 0.7967 (mmm) cc_final: 0.7182 (mmm)
REVERT: B  400 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7781 (mtt180)
REVERT: B  416 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8500 (ppp)
  outliers start: 40
  outliers final: 32
  residues processed: 225
  average time/residue: 0.2207
  time to fit residues: 69.3238
Evaluate side-chains
  235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  191 GLU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  345 GLU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  398 MET
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 112 optimal weight:   10.0000
   chunk 90 optimal weight:   40.0000
   chunk 54 optimal weight:   40.0000
   chunk 59 optimal weight:    8.9990
   chunk 70 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 80 optimal weight:   50.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 226 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.083511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.064514 restraints weight = 35093.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.066887 restraints weight = 18067.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.068412 restraints weight = 11263.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3391
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3391 r_free = 0.3391    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3391
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9865  Z= 0.249
  Angle     :  0.812  15.066  13407  Z= 0.401
  Chirality :  0.046   0.330   1505
  Planarity :  0.010   0.375   1749
  Dihedral  : 11.072 175.556   1435
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 25.15 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.32 (0.24), residues: 1172
  helix:  0.85 (0.23), residues: 481
  sheet: -0.48 (0.33), residues: 196
  loop : -1.11 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 346 
 HIS   0.006   0.001   HIS C 204 
 PHE   0.019   0.002   PHE A 149 
 TYR   0.015   0.001   TYR C  71 
 ARG   0.067   0.001   ARG C 203 

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

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

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2344 Ramachandran restraints generated.
    1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  102 TYR cc_start: 0.6975 (t80) cc_final: 0.6667 (t80)
REVERT: C  149 TYR cc_start: 0.8749 (t80) cc_final: 0.8338 (t80)
REVERT: C  151 GLU cc_start: 0.9045 (mp0) cc_final: 0.8367 (mp0)
REVERT: C  182 LYS cc_start: 0.9007 (tttp) cc_final: 0.8624 (tttp)
REVERT: C  193 LEU cc_start: 0.9164 (tp) cc_final: 0.8905 (pp)
REVERT: C  218 HIS cc_start: 0.8540 (m-70) cc_final: 0.7897 (m-70)
REVERT: C  274 GLN cc_start: 0.8995 (mt0) cc_final: 0.8421 (pp30)
REVERT: C  301 TYR cc_start: 0.9225 (m-80) cc_final: 0.8920 (m-80)
REVERT: C  305 LYS cc_start: 0.9226 (mttp) cc_final: 0.8896 (mtpt)
REVERT: C  338 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8663 (t0)
REVERT: A   86 LEU cc_start: 0.9388 (mt) cc_final: 0.9099 (mt)
REVERT: A  124 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9337 (ttpp)
REVERT: A  127 ASP cc_start: 0.8896 (m-30) cc_final: 0.8628 (m-30)
REVERT: A  224 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8212 (m-80)
REVERT: A  272 TYR cc_start: 0.8511 (t80) cc_final: 0.8168 (t80)
REVERT: A  276 ILE cc_start: 0.9410 (tp) cc_final: 0.9193 (tp)
REVERT: A  297 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: A  302 MET cc_start: 0.8548 (mtt) cc_final: 0.8051 (mtt)
REVERT: A  313 MET cc_start: 0.6591 (tpt) cc_final: 0.5926 (tpt)
REVERT: A  363 VAL cc_start: 0.8928 (t) cc_final: 0.8632 (p)
REVERT: A  372 GLN cc_start: 0.9164 (mp10) cc_final: 0.8775 (mm-40)
REVERT: A  375 VAL cc_start: 0.9410 (t) cc_final: 0.9117 (p)
REVERT: A  377 MET cc_start: 0.8053 (tmm) cc_final: 0.7556 (tmm)
REVERT: A  380 ASN cc_start: 0.8682 (t0) cc_final: 0.8180 (m-40)
REVERT: A  413 MET cc_start: 0.9174 (mmm) cc_final: 0.8816 (mmm)
REVERT: B    8 GLN cc_start: 0.8773 (mt0) cc_final: 0.8235 (mt0)
REVERT: B   68 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9145 (m)
REVERT: B  156 LYS cc_start: 0.9540 (mttt) cc_final: 0.9307 (mmtm)
REVERT: B  159 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: B  166 MET cc_start: 0.8120 (mmm) cc_final: 0.7597 (mtm)
REVERT: B  295 MET cc_start: 0.8813 (ppp) cc_final: 0.8593 (ppp)
REVERT: B  302 MET cc_start: 0.8944 (mmm) cc_final: 0.8245 (mtt)
REVERT: B  309 HIS cc_start: 0.8848 (m170) cc_final: 0.8569 (m-70)
REVERT: B  322 ARG cc_start: 0.9027 (mmm160) cc_final: 0.8614 (mmm160)
REVERT: B  323 MET cc_start: 0.8685 (mpp) cc_final: 0.7744 (mpp)
REVERT: B  325 MET cc_start: 0.8869 (mpp) cc_final: 0.8235 (mpp)
REVERT: B  332 MET cc_start: 0.9504 (mmt) cc_final: 0.9278 (mmm)
REVERT: B  373 MET cc_start: 0.7912 (mmm) cc_final: 0.7575 (mmt)
REVERT: B  400 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7762 (mtt180)
REVERT: B  416 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (ppp)
  outliers start: 38
  outliers final: 29
  residues processed: 224
  average time/residue: 0.2281
  time to fit residues: 71.1863
Evaluate side-chains
  229 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  338 ASN
Chi-restraints excluded: chain C residue  341 ASN
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  211 ASP
Chi-restraints excluded: chain B residue  220 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  353 THR
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  377 PHE
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  422 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0970
   chunk 35 optimal weight:   50.0000
   chunk 101 optimal weight:   40.0000
   chunk 85 optimal weight:   30.0000
   chunk 67 optimal weight:    1.9990
   chunk 83 optimal weight:   30.0000
   chunk 44 optimal weight:   40.0000
   chunk 97 optimal weight:   20.0000
   chunk 25 optimal weight:    3.9990
   overall best weight:    4.4186

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  35 GLN
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.085179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.065853 restraints weight = 34852.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.068214 restraints weight = 18108.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.069812 restraints weight = 11369.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9865  Z= 0.224
  Angle     :  0.866  31.045  13407  Z= 0.417
  Chirality :  0.046   0.331   1505
  Planarity :  0.010   0.404   1749
  Dihedral  : 10.955 173.103   1435
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.26 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.31 (0.24), residues: 1172
  helix:  0.86 (0.23), residues: 477
  sheet: -0.40 (0.33), residues: 201
  loop : -1.13 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 346 
 HIS   0.006   0.001   HIS A  28 
 PHE   0.016   0.001   PHE B 272 
 TYR   0.014   0.001   TYR C  93 
 ARG   0.056   0.001   ARG C 203 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3069.53 seconds
wall clock time: 55 minutes 55.94 seconds (3355.94 seconds total)