Starting phenix.real_space_refine
on Mon Nov 17 18:14:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mi7_9125/11_2025/6mi7_9125.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      43      5.16       5
     C    4713      2.51       5
     N    1240      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7285
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "F"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1695
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 9, 'TRANS': 207}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1778
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 12, 'TRANS': 217}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1787
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
    Chain: "B"
      Number of atoms: 1787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1787
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
    Chain: "C"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 187
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "F"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'PGT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.04, per 1000 atoms: 0.28
  Number of scatterers: 7285
  At special positions: 0
  Unit cell: (81.18, 102.09, 109.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P       1     15.00
     O    1288      8.00
     N    1240      7.00
     C    4713      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=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 385.9 milliseconds
  

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      51.5% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'F' and resid 2 through 9
      removed outlier: 3.553A  pdb=" N   LEU F   7 " --> pdb=" O   ILE F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 10 through 24
      removed outlier: 3.709A  pdb=" N   LEU F  16 " --> pdb=" O   LEU F  12 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ALA F  17 " --> pdb=" O   LYS F  13 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE F  21 " --> pdb=" O   ALA F  17 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 47 through 52
    Processing helix  chain 'F' and resid 55 through 59
    Processing helix  chain 'F' and resid 63 through 82
      removed outlier: 3.569A  pdb=" N   PHE F  69 " --> pdb=" O   PRO F  65 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU F  79 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU F  82 " --> pdb=" O   LYS F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 84 through 89
      removed outlier: 3.670A  pdb=" N   MET F  88 " --> pdb=" O   GLU F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 95 through 119
      removed outlier: 3.551A  pdb=" N   VAL F  99 " --> pdb=" O   LYS F  95 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE F 104 " --> pdb=" O   LYS F 100 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   PHE F 108 " --> pdb=" O   ILE F 104 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR F 109 " --> pdb=" O   LEU F 105 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL F 112 " --> pdb=" O   PHE F 108 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL F 117 " --> pdb=" O   ALA F 113 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 126
    Processing helix  chain 'F' and resid 269 through 284
      removed outlier: 3.546A  pdb=" N   VAL F 273 " --> pdb=" O   ARG F 269 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR F 275 " --> pdb=" O   THR F 271 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   VAL F 276 " --> pdb=" O   LEU F 272 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE F 277 " --> pdb=" O   VAL F 273 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   MET F 278 " --> pdb=" O   PHE F 274 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA F 280 " --> pdb=" O   VAL F 276 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   LEU F 281 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   VAL F 284 " --> pdb=" O   ALA F 280 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 294 through 299
    Processing helix  chain 'F' and resid 299 through 319
      removed outlier: 3.896A  pdb=" N   LEU F 305 " --> pdb=" O   PRO F 301 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN F 313 " --> pdb=" O   PHE F 309 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   THR F 314 " --> pdb=" O   PHE F 310 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   LYS F 317 " --> pdb=" O   GLN F 313 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 331 through 345
      removed outlier: 3.703A  pdb=" N   TYR F 338 " --> pdb=" O   VAL F 334 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 33
      removed outlier: 3.533A  pdb=" N   ILE G  11 " --> pdb=" O   LEU G   7 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY G  12 " --> pdb=" O   ASP G   8 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS G  13 " --> pdb=" O   ARG G   9 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   MET G  20 " --> pdb=" O   PHE G  16 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU G  23 " --> pdb=" O   ILE G  19 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU G  26 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE G  33 " --> pdb=" O   LEU G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 59
    Processing helix  chain 'G' and resid 59 through 64
      removed outlier: 4.114A  pdb=" N   ASP G  63 " --> pdb=" O   SER G  59 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL G  64 " --> pdb=" O   VAL G  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 59 through 64'
    Processing helix  chain 'G' and resid 77 through 82
    Processing helix  chain 'G' and resid 88 through 93
    Processing helix  chain 'G' and resid 94 through 96
      No H-bonds generated for 'chain 'G' and resid 94 through 96'
    Processing helix  chain 'G' and resid 98 through 109
      removed outlier: 3.648A  pdb=" N   VAL G 102 " --> pdb=" O   THR G  98 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL G 106 " --> pdb=" O   VAL G 102 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET G 107 " --> pdb=" O   ALA G 103 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 110 through 123
      removed outlier: 3.898A  pdb=" N   LEU G 115 " --> pdb=" O   ILE G 111 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LEU G 116 " --> pdb=" O   PRO G 112 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE G 120 " --> pdb=" O   LEU G 116 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLY G 121 " --> pdb=" O   THR G 117 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLU G 122 " --> pdb=" O   MET G 118 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 124 through 131
      removed outlier: 3.723A  pdb=" N   MET G 131 " --> pdb=" O   GLN G 127 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 131 through 136
      removed outlier: 3.580A  pdb=" N   ARG G 136 " --> pdb=" O   ALA G 132 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 269 through 280
      removed outlier: 3.578A  pdb=" N   LEU G 273 " --> pdb=" O   GLY G 269 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS G 278 " --> pdb=" O   ASN G 274 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE G 280 " --> pdb=" O   TRP G 276 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 282 through 293
      removed outlier: 4.038A  pdb=" N   ALA G 286 " --> pdb=" O   PRO G 282 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LEU G 290 " --> pdb=" O   ALA G 286 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 306 through 318
      removed outlier: 4.420A  pdb=" N   GLY G 316 " --> pdb=" O   GLY G 312 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL G 318 " --> pdb=" O   SER G 314 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 319 through 324
      removed outlier: 3.521A  pdb=" N   GLN G 324 " --> pdb=" O   TYR G 320 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 325 through 333
      removed outlier: 3.651A  pdb=" N   THR G 330 " --> pdb=" O   PHE G 326 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 343 through 356
      removed outlier: 3.851A  pdb=" N   PHE G 348 " --> pdb=" O   PRO G 344 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   PHE G 349 " --> pdb=" O   SER G 345 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE G 351 " --> pdb=" O   SER G 347 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   SER G 352 " --> pdb=" O   PHE G 348 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU G 356 " --> pdb=" O   SER G 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 51
      removed outlier: 3.635A  pdb=" N   MET A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 74 through 79
    Processing helix  chain 'A' and resid 94 through 100
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.712A  pdb=" N   GLN A 104 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 123
      removed outlier: 3.578A  pdb=" N   ASP A 116 " --> pdb=" O   GLU A 112 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA A 118 " --> pdb=" O   ARG A 114 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 153
      removed outlier: 4.068A  pdb=" N   ARG A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   ARG A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 142 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA A 151 " --> pdb=" O   GLU A 147 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 186
      removed outlier: 3.916A  pdb=" N   ILE A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   SER A 186 " --> pdb=" O   HIS A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 3.721A  pdb=" N   THR A 200 " --> pdb=" O   ASN A 196 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 196 through 201'
    Processing helix  chain 'B' and resid 41 through 50
      removed outlier: 3.502A  pdb=" N   THR B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 76
      removed outlier: 3.996A  pdb=" N   ALA B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 103
      removed outlier: 3.587A  pdb=" N   MET B 100 " --> pdb=" O   TYR B  96 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 101 " --> pdb=" O   ASP B  97 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL B 102 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 125
      removed outlier: 4.171A  pdb=" N   ALA B 118 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ASN B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU B 123 " --> pdb=" O   ASN B 119 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLU B 124 " --> pdb=" O   GLU B 120 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   PHE B 125 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 153
      removed outlier: 3.773A  pdb=" N   ILE B 148 " --> pdb=" O   ARG B 144 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ALA B 151 " --> pdb=" O   GLU B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 183
      removed outlier: 3.572A  pdb=" N   ARG B 178 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE B 179 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.589A  pdb=" N   LEU B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'C' and resid 4 through 21
      removed outlier: 3.876A  pdb=" N   ILE C   9 " --> pdb=" O   ARG C   5 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   ILE C  10 " --> pdb=" O   ARG C   6 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL C  11 " --> pdb=" O   TRP C   7 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER C  13 " --> pdb=" O   ILE C   9 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   MET C  19 " --> pdb=" O   ALA C  15 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY C  21 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 27
      removed outlier: 5.269A  pdb=" N   LEU A   9 " --> pdb=" O   ASP A  21 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   SER A  23 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   LYS A   7 " --> pdb=" O   SER A  23 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   THR A  25 " --> pdb=" O   THR A   5 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   THR A   5 " --> pdb=" O   THR A  25 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   ASN A  27 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   THR A   3 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82
      removed outlier: 7.297A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 209 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19
      removed outlier: 6.526A  pdb=" N   LYS B  11 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE B  61 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   LEU B   9 " --> pdb=" O   ALA B  57 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 33
      removed outlier: 3.809A  pdb=" N   LEU B 191 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR B 193 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   GLY B  81 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ASP B 162 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU B  83 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)

    229 hydrogen bonds defined for protein.
    660 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: 0.78

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2100
        1.33 -     1.45: 1009
        1.45 -     1.57: 4213
        1.57 -     1.69: 2
        1.69 -     1.81: 82
  Bond restraints: 7406
  Sorted by residual:
  bond pdb=" C11 PGT F 401 "
       pdb=" O3  PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.452 -0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" C31 PGT F 401 "
       pdb=" O2  PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.331  1.450 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C   LEU F 300 "
       pdb=" N   PRO F 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.65e+00
  bond pdb=" O3P PGT F 401 "
       pdb=" P   PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.640  1.603  0.037 2.00e-02 2.50e+03 3.50e+00
  bond pdb=" O4P PGT F 401 "
       pdb=" P   PGT F 401 "
    ideal  model  delta    sigma   weight residual
    1.641  1.606  0.035 2.00e-02 2.50e+03 3.06e+00
  ... (remaining 7401 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 9673
        2.72 -     5.45: 263
        5.45 -     8.17: 63
        8.17 -    10.89: 22
       10.89 -    13.61: 2
  Bond angle restraints: 10023
  Sorted by residual:
  angle pdb=" N   VAL B 230 "
        pdb=" CA  VAL B 230 "
        pdb=" C   VAL B 230 "
      ideal   model   delta    sigma   weight residual
     113.71  106.45    7.26 9.50e-01 1.11e+00 5.84e+01
  angle pdb=" N   ILE A 171 "
        pdb=" CA  ILE A 171 "
        pdb=" C   ILE A 171 "
      ideal   model   delta    sigma   weight residual
     111.91  105.59    6.32 8.90e-01 1.26e+00 5.04e+01
  angle pdb=" N   ILE B 216 "
        pdb=" CA  ILE B 216 "
        pdb=" C   ILE B 216 "
      ideal   model   delta    sigma   weight residual
     112.43  107.05    5.38 9.20e-01 1.18e+00 3.42e+01
  angle pdb=" N   VAL A 230 "
        pdb=" CA  VAL A 230 "
        pdb=" C   VAL A 230 "
      ideal   model   delta    sigma   weight residual
     112.80  106.98    5.82 1.15e+00 7.56e-01 2.56e+01
  angle pdb=" C   LEU F 266 "
        pdb=" N   ASN F 267 "
        pdb=" CA  ASN F 267 "
      ideal   model   delta    sigma   weight residual
     121.54  130.54   -9.00 1.91e+00 2.74e-01 2.22e+01
  ... (remaining 10018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.94: 4316
       25.94 -    51.88: 164
       51.88 -    77.82: 11
       77.82 -   103.76: 0
      103.76 -   129.70: 1
  Dihedral angle restraints: 4492
    sinusoidal: 1817
      harmonic: 2675
  Sorted by residual:
  dihedral pdb=" CA  ASN F 290 "
           pdb=" C   ASN F 290 "
           pdb=" N   PRO F 291 "
           pdb=" CA  PRO F 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.24  -32.76     0      5.00e+00 4.00e-02 4.29e+01
  dihedral pdb=" CA  PHE B  90 "
           pdb=" C   PHE B  90 "
           pdb=" N   ARG B  91 "
           pdb=" CA  ARG B  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.88  -26.12     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE G 280 "
           pdb=" C   PHE G 280 "
           pdb=" N   GLN G 281 "
           pdb=" CA  GLN G 281 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 4489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1074
       0.090 -    0.179: 116
       0.179 -    0.269: 11
       0.269 -    0.358: 3
       0.358 -    0.448: 1
  Chirality restraints: 1205
  Sorted by residual:
  chirality pdb=" CB  ILE A 105 "
            pdb=" CA  ILE A 105 "
            pdb=" CG1 ILE A 105 "
            pdb=" CG2 ILE A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.45 2.00e-01 2.50e+01 5.01e+00
  chirality pdb=" CB  ILE A  62 "
            pdb=" CA  ILE A  62 "
            pdb=" CG1 ILE A  62 "
            pdb=" CG2 ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CB  VAL G 258 "
            pdb=" CA  VAL G 258 "
            pdb=" CG1 VAL G 258 "
            pdb=" CG2 VAL G 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 1202 not shown)

  Planarity restraints: 1246
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 284 "   -0.045 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO F 285 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO F 285 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F 285 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY G 327 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.76e+00
        pdb=" N   PRO G 328 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO G 328 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO G 328 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G 335 "    0.043 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO G 336 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO G 336 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO G 336 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1243 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 62
        2.62 -     3.19: 6058
        3.19 -     3.76: 10728
        3.76 -     4.33: 14294
        4.33 -     4.90: 22444
  Nonbonded interactions: 53586
  Sorted by model distance:
  nonbonded pdb=" O1P PGT F 401 "
            pdb=" O5  PGT F 401 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" OG1 THR A 220 "
            pdb=" OE1 GLU A 223 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR A  96 "
            pdb=" OE1 GLU A 115 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   SER A  88 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OE2 GLU F  82 "
            pdb=" NH1 ARG B  91 "
     model   vdw
     2.353 3.120
  ... (remaining 53581 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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   0.125   7406  Z= 0.261
  Angle     :  1.187  13.614  10023  Z= 0.592
  Chirality :  0.062   0.448   1205
  Planarity :  0.008   0.067   1246
  Dihedral  : 12.825 129.702   2760
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  9.29 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.97 (0.19), residues: 911
  helix: -4.39 (0.11), residues: 436
  sheet: -3.55 (0.43), residues: 78
  loop : -3.37 (0.25), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 143 
 TYR   0.039   0.002   TYR F  80 
 PHE   0.039   0.003   PHE G  67 
 TRP   0.014   0.002   TRP G 276 
 HIS   0.009   0.001   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 7406)
  covalent geometry    : angle       1.18682 (10023)
  hydrogen bonds       : bond        0.30556 (  229)
  hydrogen bonds       : angle      10.41381 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 373
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    6 TYR cc_start: 0.9254 (t80) cc_final: 0.8529 (t80)
REVERT: F   59 MET cc_start: 0.5990 (tpp) cc_final: 0.5543 (ptt)
REVERT: F   78 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7677 (ttmt)
REVERT: F  281 LEU cc_start: 0.9068 (tt) cc_final: 0.8755 (tt)
REVERT: F  297 LEU cc_start: 0.9472 (tp) cc_final: 0.9253 (tp)
REVERT: F  314 THR cc_start: 0.9276 (p) cc_final: 0.8947 (m)
REVERT: G   90 VAL cc_start: 0.9491 (m) cc_final: 0.9180 (t)
REVERT: G  100 MET cc_start: 0.7296 (tpp) cc_final: 0.6866 (tpp)
REVERT: G  108 LYS cc_start: 0.7410 (tmtt) cc_final: 0.6753 (tttt)
REVERT: G  254 LEU cc_start: 0.9044 (tp) cc_final: 0.8818 (mm)
REVERT: G  278 LYS cc_start: 0.9115 (ttmp) cc_final: 0.8825 (mtpt)
REVERT: G  351 ILE cc_start: 0.9169 (mt) cc_final: 0.8928 (mt)
REVERT: G  356 LEU cc_start: 0.7557 (pp) cc_final: 0.7352 (pp)
REVERT: A    8 ASN cc_start: 0.8481 (m110) cc_final: 0.8089 (m110)
REVERT: A   11 LYS cc_start: 0.8850 (tptp) cc_final: 0.8180 (tptm)
REVERT: A   21 ASP cc_start: 0.7834 (t0) cc_final: 0.7451 (p0)
REVERT: A   98 ASN cc_start: 0.8835 (t0) cc_final: 0.8404 (t0)
REVERT: A  104 GLN cc_start: 0.8545 (mt0) cc_final: 0.8334 (mm110)
REVERT: A  108 ASP cc_start: 0.9002 (p0) cc_final: 0.8693 (p0)
REVERT: A  116 ASP cc_start: 0.7986 (m-30) cc_final: 0.7679 (t0)
REVERT: A  123 GLU cc_start: 0.8180 (pt0) cc_final: 0.6571 (tm-30)
REVERT: A  128 GLU cc_start: 0.7529 (pm20) cc_final: 0.6904 (pm20)
REVERT: A  137 SER cc_start: 0.8660 (p) cc_final: 0.8417 (p)
REVERT: A  155 ASN cc_start: 0.7942 (t0) cc_final: 0.7655 (t0)
REVERT: A  162 ASP cc_start: 0.9049 (t0) cc_final: 0.8799 (t0)
REVERT: A  185 ASP cc_start: 0.8635 (t70) cc_final: 0.8207 (t0)
REVERT: A  220 THR cc_start: 0.7163 (p) cc_final: 0.6933 (m)
REVERT: B   19 VAL cc_start: 0.9139 (t) cc_final: 0.8878 (t)
REVERT: B   44 THR cc_start: 0.8961 (m) cc_final: 0.8626 (m)
REVERT: B   82 TYR cc_start: 0.9066 (t80) cc_final: 0.8634 (t80)
REVERT: B   95 VAL cc_start: 0.9148 (t) cc_final: 0.8935 (p)
REVERT: B  100 MET cc_start: 0.8361 (mmm) cc_final: 0.7932 (mmm)
REVERT: B  113 GLN cc_start: 0.7647 (pm20) cc_final: 0.7365 (pm20)
REVERT: B  121 LEU cc_start: 0.9155 (tp) cc_final: 0.8823 (tt)
REVERT: B  126 HIS cc_start: 0.8155 (m-70) cc_final: 0.7482 (m170)
REVERT: B  145 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8558 (mtm180)
REVERT: B  169 ASP cc_start: 0.8616 (p0) cc_final: 0.8409 (p0)
REVERT: C    6 ARG cc_start: 0.7707 (mtp180) cc_final: 0.5994 (ptt180)
  outliers start: 3
  outliers final: 0
  residues processed: 374
  average time/residue: 0.0908
  time to fit residues: 44.4450
Evaluate side-chains
  264 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
G  85 GLN
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.141349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.116284 restraints weight = 12299.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118895 restraints weight = 8040.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.120511 restraints weight = 6005.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121851 restraints weight = 4974.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.122421 restraints weight = 4351.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7406  Z= 0.155
  Angle     :  0.747  10.309  10023  Z= 0.378
  Chirality :  0.045   0.243   1205
  Planarity :  0.006   0.048   1246
  Dihedral  :  9.235 115.565   1050
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.34 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.54 (0.23), residues: 911
  helix: -2.93 (0.19), residues: 457
  sheet: -3.09 (0.48), residues: 68
  loop : -2.94 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 106 
 TYR   0.022   0.001   TYR F  80 
 PHE   0.040   0.002   PHE G  67 
 TRP   0.015   0.001   TRP F 330 
 HIS   0.004   0.001   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7406)
  covalent geometry    : angle       0.74656 (10023)
  hydrogen bonds       : bond        0.04751 (  229)
  hydrogen bonds       : angle       6.05820 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 327
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    5 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8021 (ttp80)
REVERT: F   26 PHE cc_start: 0.7666 (m-10) cc_final: 0.7434 (m-10)
REVERT: F   59 MET cc_start: 0.5932 (tpp) cc_final: 0.5315 (ptt)
REVERT: F  105 LEU cc_start: 0.9236 (pp) cc_final: 0.8982 (pp)
REVERT: F  282 MET cc_start: 0.8803 (ptm) cc_final: 0.8562 (ttp)
REVERT: G   20 MET cc_start: 0.6860 (tmm) cc_final: 0.6418 (tmm)
REVERT: G   90 VAL cc_start: 0.9529 (m) cc_final: 0.9140 (t)
REVERT: G  100 MET cc_start: 0.7288 (tpp) cc_final: 0.7015 (tpp)
REVERT: G  108 LYS cc_start: 0.7323 (tmtt) cc_final: 0.6931 (tttt)
REVERT: G  113 LEU cc_start: 0.9307 (tp) cc_final: 0.9051 (tt)
REVERT: G  120 ILE cc_start: 0.8916 (pt) cc_final: 0.8525 (mm)
REVERT: G  356 LEU cc_start: 0.7864 (pp) cc_final: 0.7565 (pp)
REVERT: G  357 MET cc_start: 0.7649 (mmt) cc_final: 0.7394 (mmt)
REVERT: A    9 LEU cc_start: 0.9278 (mt) cc_final: 0.8980 (mp)
REVERT: A   98 ASN cc_start: 0.8747 (t0) cc_final: 0.8336 (t0)
REVERT: A  116 ASP cc_start: 0.7946 (m-30) cc_final: 0.7638 (t0)
REVERT: A  123 GLU cc_start: 0.8181 (pt0) cc_final: 0.6936 (tm-30)
REVERT: A  128 GLU cc_start: 0.7523 (pm20) cc_final: 0.6802 (pm20)
REVERT: A  155 ASN cc_start: 0.8108 (t0) cc_final: 0.7816 (t0)
REVERT: A  185 ASP cc_start: 0.8499 (t70) cc_final: 0.8219 (t0)
REVERT: A  220 THR cc_start: 0.7744 (p) cc_final: 0.6635 (p)
REVERT: B    8 ASN cc_start: 0.7825 (m110) cc_final: 0.6757 (m110)
REVERT: B   67 ILE cc_start: 0.9213 (pt) cc_final: 0.8957 (pt)
REVERT: B   82 TYR cc_start: 0.8859 (t80) cc_final: 0.8423 (t80)
REVERT: B  121 LEU cc_start: 0.8892 (tp) cc_final: 0.8661 (tt)
REVERT: B  126 HIS cc_start: 0.8181 (m-70) cc_final: 0.7079 (m170)
REVERT: B  145 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8354 (mtp85)
REVERT: B  169 ASP cc_start: 0.8809 (p0) cc_final: 0.8532 (p0)
REVERT: B  196 ASN cc_start: 0.8378 (t0) cc_final: 0.8161 (t0)
REVERT: C    6 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6194 (ptt180)
  outliers start: 2
  outliers final: 0
  residues processed: 329
  average time/residue: 0.0776
  time to fit residues: 34.6697
Evaluate side-chains
  255 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  98 ASN
B 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.142072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.117273 restraints weight = 12156.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.119902 restraints weight = 7913.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121626 restraints weight = 5908.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122904 restraints weight = 4857.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.123514 restraints weight = 4249.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7406  Z= 0.137
  Angle     :  0.705  11.065  10023  Z= 0.353
  Chirality :  0.044   0.238   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  8.426  98.859   1050
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.72 (0.25), residues: 911
  helix: -2.16 (0.22), residues: 464
  sheet: -2.81 (0.50), residues: 68
  loop : -2.65 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 133 
 TYR   0.029   0.001   TYR F  80 
 PHE   0.028   0.002   PHE G  67 
 TRP   0.011   0.001   TRP F 330 
 HIS   0.004   0.001   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7406)
  covalent geometry    : angle       0.70459 (10023)
  hydrogen bonds       : bond        0.03915 (  229)
  hydrogen bonds       : angle       5.49830 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 313
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.6076 (tpp) cc_final: 0.5370 (ptt)
REVERT: F   68 LEU cc_start: 0.9158 (tp) cc_final: 0.8775 (tt)
REVERT: F  105 LEU cc_start: 0.9144 (pp) cc_final: 0.8922 (pp)
REVERT: G   20 MET cc_start: 0.6815 (tmm) cc_final: 0.6491 (tmm)
REVERT: G   78 LEU cc_start: 0.9040 (tp) cc_final: 0.8836 (tt)
REVERT: G   90 VAL cc_start: 0.9567 (m) cc_final: 0.9213 (t)
REVERT: G  100 MET cc_start: 0.7494 (tpp) cc_final: 0.6991 (tpp)
REVERT: G  108 LYS cc_start: 0.7428 (tmtt) cc_final: 0.6823 (tttt)
REVERT: G  120 ILE cc_start: 0.8989 (pt) cc_final: 0.8684 (mm)
REVERT: G  356 LEU cc_start: 0.7818 (pp) cc_final: 0.7533 (pp)
REVERT: G  357 MET cc_start: 0.7699 (mmt) cc_final: 0.7391 (mmt)
REVERT: A    9 LEU cc_start: 0.9386 (mt) cc_final: 0.9111 (mt)
REVERT: A   48 MET cc_start: 0.8056 (ttm) cc_final: 0.7607 (ttp)
REVERT: A   98 ASN cc_start: 0.8728 (t0) cc_final: 0.8382 (t0)
REVERT: A  116 ASP cc_start: 0.8087 (m-30) cc_final: 0.7704 (t0)
REVERT: A  123 GLU cc_start: 0.8211 (pt0) cc_final: 0.7378 (tm-30)
REVERT: A  128 GLU cc_start: 0.7638 (pm20) cc_final: 0.6622 (pm20)
REVERT: A  155 ASN cc_start: 0.8221 (t0) cc_final: 0.7939 (t0)
REVERT: A  220 THR cc_start: 0.7911 (p) cc_final: 0.6647 (t)
REVERT: B   67 ILE cc_start: 0.9078 (pt) cc_final: 0.8846 (pt)
REVERT: B   68 SER cc_start: 0.8738 (m) cc_final: 0.8216 (p)
REVERT: B   82 TYR cc_start: 0.8843 (t80) cc_final: 0.8437 (t80)
REVERT: B  100 MET cc_start: 0.7754 (mmm) cc_final: 0.7388 (mmm)
REVERT: B  126 HIS cc_start: 0.8231 (m-70) cc_final: 0.7479 (m170)
REVERT: B  145 ARG cc_start: 0.9159 (mtm-85) cc_final: 0.8500 (mtm180)
REVERT: B  169 ASP cc_start: 0.8799 (p0) cc_final: 0.8548 (p0)
REVERT: C    6 ARG cc_start: 0.7047 (mtp180) cc_final: 0.5900 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 314
  average time/residue: 0.0815
  time to fit residues: 34.5863
Evaluate side-chains
  253 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 4 optimal weight:    4.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  85 GLN
** B  73 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 = 0.3590 r_free = 0.3590 target = 0.143051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.117909 restraints weight = 12417.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.120322 restraints weight = 8286.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.121916 restraints weight = 6323.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.123122 restraints weight = 5278.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.123827 restraints weight = 4679.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7406  Z= 0.121
  Angle     :  0.691  10.292  10023  Z= 0.340
  Chirality :  0.044   0.223   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  7.999  95.142   1050
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  3.94 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.26), residues: 911
  helix: -1.70 (0.23), residues: 456
  sheet: -2.26 (0.52), residues: 68
  loop : -2.41 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 133 
 TYR   0.021   0.001   TYR F  80 
 PHE   0.019   0.001   PHE A 165 
 TRP   0.008   0.001   TRP F 330 
 HIS   0.003   0.001   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7406)
  covalent geometry    : angle       0.69063 (10023)
  hydrogen bonds       : bond        0.03478 (  229)
  hydrogen bonds       : angle       5.15550 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 313
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5875 (tpp) cc_final: 0.5376 (ptt)
REVERT: G   20 MET cc_start: 0.7073 (tmm) cc_final: 0.6694 (tmm)
REVERT: G   90 VAL cc_start: 0.9458 (m) cc_final: 0.9176 (t)
REVERT: G   93 GLN cc_start: 0.9279 (tp40) cc_final: 0.9022 (tt0)
REVERT: G  100 MET cc_start: 0.7633 (tpp) cc_final: 0.7387 (tpp)
REVERT: G  108 LYS cc_start: 0.7669 (tmtt) cc_final: 0.6981 (tttt)
REVERT: G  118 MET cc_start: 0.8007 (mmm) cc_final: 0.7773 (mmt)
REVERT: G  120 ILE cc_start: 0.8965 (pt) cc_final: 0.8617 (mm)
REVERT: G  357 MET cc_start: 0.7795 (mmt) cc_final: 0.7497 (mmt)
REVERT: A    9 LEU cc_start: 0.9420 (mt) cc_final: 0.9136 (mm)
REVERT: A   42 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8128 (mtmm)
REVERT: A   98 ASN cc_start: 0.8692 (t0) cc_final: 0.8356 (t0)
REVERT: A  107 ASP cc_start: 0.7822 (p0) cc_final: 0.7196 (m-30)
REVERT: A  128 GLU cc_start: 0.7574 (pm20) cc_final: 0.7360 (pm20)
REVERT: A  155 ASN cc_start: 0.8128 (t0) cc_final: 0.7908 (t0)
REVERT: B    8 ASN cc_start: 0.7935 (m110) cc_final: 0.6777 (m-40)
REVERT: B   67 ILE cc_start: 0.9163 (pt) cc_final: 0.8904 (pt)
REVERT: B   68 SER cc_start: 0.8749 (m) cc_final: 0.8333 (p)
REVERT: B   82 TYR cc_start: 0.8758 (t80) cc_final: 0.8316 (t80)
REVERT: B  113 GLN cc_start: 0.7419 (pm20) cc_final: 0.7088 (pm20)
REVERT: B  126 HIS cc_start: 0.7944 (m-70) cc_final: 0.7343 (m170)
REVERT: B  145 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8456 (mtm180)
REVERT: B  169 ASP cc_start: 0.8651 (p0) cc_final: 0.8445 (p0)
REVERT: B  186 SER cc_start: 0.9096 (m) cc_final: 0.8673 (p)
REVERT: C    6 ARG cc_start: 0.7384 (mtp180) cc_final: 0.6279 (ptm-80)
  outliers start: 2
  outliers final: 0
  residues processed: 315
  average time/residue: 0.0851
  time to fit residues: 36.2771
Evaluate side-chains
  247 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0570
   chunk 5 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN
** B  73 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 = 0.3577 r_free = 0.3577 target = 0.141165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.116066 restraints weight = 12345.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.118754 restraints weight = 8041.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120551 restraints weight = 5972.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.121671 restraints weight = 4885.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.122626 restraints weight = 4299.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7406  Z= 0.114
  Angle     :  0.691  13.729  10023  Z= 0.334
  Chirality :  0.044   0.234   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  7.711  89.567   1050
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.27), residues: 911
  helix: -1.36 (0.24), residues: 460
  sheet: -1.60 (0.65), residues: 48
  loop : -2.32 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 133 
 TYR   0.030   0.001   TYR F  80 
 PHE   0.025   0.002   PHE G  67 
 TRP   0.007   0.001   TRP F 330 
 HIS   0.003   0.000   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7406)
  covalent geometry    : angle       0.69068 (10023)
  hydrogen bonds       : bond        0.03223 (  229)
  hydrogen bonds       : angle       4.92232 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 307
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5884 (tpp) cc_final: 0.5391 (ptt)
REVERT: F   78 LYS cc_start: 0.8326 (tttt) cc_final: 0.7577 (tptt)
REVERT: F  282 MET cc_start: 0.8940 (ttp) cc_final: 0.8469 (tmm)
REVERT: G   15 ILE cc_start: 0.9372 (mm) cc_final: 0.8995 (mt)
REVERT: G   20 MET cc_start: 0.7058 (tmm) cc_final: 0.6816 (tmm)
REVERT: G   28 SER cc_start: 0.8803 (m) cc_final: 0.8191 (t)
REVERT: G   62 LYS cc_start: 0.8788 (tptt) cc_final: 0.8574 (tptm)
REVERT: G   90 VAL cc_start: 0.9502 (m) cc_final: 0.9178 (t)
REVERT: G  100 MET cc_start: 0.7599 (tpp) cc_final: 0.7018 (tpp)
REVERT: G  108 LYS cc_start: 0.7637 (tmtt) cc_final: 0.6927 (tttt)
REVERT: G  120 ILE cc_start: 0.8918 (pt) cc_final: 0.8688 (mm)
REVERT: G  357 MET cc_start: 0.7760 (mmt) cc_final: 0.7499 (mmt)
REVERT: A    9 LEU cc_start: 0.9343 (mt) cc_final: 0.9100 (mm)
REVERT: A   42 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8146 (mtmm)
REVERT: A  107 ASP cc_start: 0.7758 (p0) cc_final: 0.7030 (m-30)
REVERT: A  155 ASN cc_start: 0.8111 (t0) cc_final: 0.7911 (t0)
REVERT: A  162 ASP cc_start: 0.9205 (t0) cc_final: 0.8977 (t0)
REVERT: A  220 THR cc_start: 0.6800 (t) cc_final: 0.4971 (m)
REVERT: B   67 ILE cc_start: 0.9079 (pt) cc_final: 0.8860 (pt)
REVERT: B   68 SER cc_start: 0.8753 (m) cc_final: 0.8391 (p)
REVERT: B   82 TYR cc_start: 0.8723 (t80) cc_final: 0.8307 (t80)
REVERT: B  113 GLN cc_start: 0.7360 (pm20) cc_final: 0.7061 (pm20)
REVERT: B  122 MET cc_start: 0.8363 (mtm) cc_final: 0.7955 (mtm)
REVERT: B  126 HIS cc_start: 0.8030 (m-70) cc_final: 0.7547 (m170)
REVERT: B  145 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8392 (mtm180)
REVERT: B  169 ASP cc_start: 0.8494 (p0) cc_final: 0.8246 (p0)
REVERT: B  183 LEU cc_start: 0.9293 (pp) cc_final: 0.9078 (tt)
REVERT: B  186 SER cc_start: 0.9041 (m) cc_final: 0.8704 (p)
REVERT: C    6 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6266 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 307
  average time/residue: 0.0839
  time to fit residues: 34.8964
Evaluate side-chains
  246 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 63 optimal weight:    0.2980
   chunk 41 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 87 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
G  85 GLN
A 136 GLN
** B  73 HIS ** 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 = 0.3636 r_free = 0.3636 target = 0.146195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.121890 restraints weight = 12286.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.124475 restraints weight = 8086.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.126292 restraints weight = 6052.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.127371 restraints weight = 4972.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.128270 restraints weight = 4385.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7406  Z= 0.114
  Angle     :  0.681  11.792  10023  Z= 0.329
  Chirality :  0.044   0.237   1205
  Planarity :  0.005   0.048   1246
  Dihedral  :  7.476  86.821   1050
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.42 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.27), residues: 911
  helix: -1.17 (0.24), residues: 466
  sheet: -1.20 (0.75), residues: 38
  loop : -2.13 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 133 
 TYR   0.011   0.001   TYR G  55 
 PHE   0.026   0.001   PHE G  67 
 TRP   0.006   0.001   TRP F 268 
 HIS   0.003   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7406)
  covalent geometry    : angle       0.68091 (10023)
  hydrogen bonds       : bond        0.03001 (  229)
  hydrogen bonds       : angle       4.74850 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 301
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5901 (tpp) cc_final: 0.5345 (ptt)
REVERT: F  282 MET cc_start: 0.9003 (ttp) cc_final: 0.8448 (tmm)
REVERT: G   28 SER cc_start: 0.8690 (m) cc_final: 0.8133 (t)
REVERT: G   82 MET cc_start: 0.7790 (ptt) cc_final: 0.7520 (ptp)
REVERT: G  100 MET cc_start: 0.7515 (tpp) cc_final: 0.6940 (tpp)
REVERT: G  108 LYS cc_start: 0.7606 (tmtt) cc_final: 0.6945 (tttt)
REVERT: G  120 ILE cc_start: 0.8899 (pt) cc_final: 0.8628 (mm)
REVERT: A    9 LEU cc_start: 0.9312 (mt) cc_final: 0.8541 (mt)
REVERT: A   42 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8216 (mtmm)
REVERT: A   48 MET cc_start: 0.8108 (ttm) cc_final: 0.7370 (ttm)
REVERT: A  107 ASP cc_start: 0.7758 (p0) cc_final: 0.6976 (m-30)
REVERT: A  123 GLU cc_start: 0.8129 (pt0) cc_final: 0.7216 (tm-30)
REVERT: B    8 ASN cc_start: 0.8011 (m110) cc_final: 0.6797 (m-40)
REVERT: B   82 TYR cc_start: 0.8787 (t80) cc_final: 0.8311 (t80)
REVERT: B  100 MET cc_start: 0.7301 (mmm) cc_final: 0.6975 (mmm)
REVERT: B  122 MET cc_start: 0.8388 (mtm) cc_final: 0.8017 (mtm)
REVERT: B  126 HIS cc_start: 0.8077 (m-70) cc_final: 0.7547 (m170)
REVERT: B  145 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8457 (mtm180)
REVERT: B  169 ASP cc_start: 0.8544 (p0) cc_final: 0.8339 (p0)
REVERT: B  186 SER cc_start: 0.9023 (m) cc_final: 0.8696 (p)
REVERT: C    6 ARG cc_start: 0.6943 (mtp180) cc_final: 0.6167 (ptm160)
  outliers start: 1
  outliers final: 0
  residues processed: 302
  average time/residue: 0.0806
  time to fit residues: 33.0303
Evaluate side-chains
  248 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0170
   chunk 35 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   chunk 82 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 67 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
A 104 GLN
** B  73 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 = 0.3617 r_free = 0.3617 target = 0.144543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.119622 restraints weight = 12364.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.122337 restraints weight = 8004.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124199 restraints weight = 5947.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.125272 restraints weight = 4872.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.126279 restraints weight = 4297.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7406  Z= 0.111
  Angle     :  0.684  11.065  10023  Z= 0.329
  Chirality :  0.044   0.218   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.266  84.081   1050
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.28), residues: 911
  helix: -0.95 (0.25), residues: 462
  sheet: -1.51 (0.65), residues: 58
  loop : -2.05 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 133 
 TYR   0.018   0.001   TYR B  96 
 PHE   0.024   0.001   PHE G  67 
 TRP   0.006   0.001   TRP F 268 
 HIS   0.002   0.000   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 7406)
  covalent geometry    : angle       0.68443 (10023)
  hydrogen bonds       : bond        0.02836 (  229)
  hydrogen bonds       : angle       4.69261 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 306
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5710 (tpp) cc_final: 0.5224 (ptt)
REVERT: F  282 MET cc_start: 0.8842 (ttp) cc_final: 0.8332 (tmm)
REVERT: G   15 ILE cc_start: 0.9393 (mm) cc_final: 0.9028 (mt)
REVERT: G   20 MET cc_start: 0.6826 (tmm) cc_final: 0.6527 (tmm)
REVERT: G   28 SER cc_start: 0.8663 (m) cc_final: 0.8193 (t)
REVERT: G   62 LYS cc_start: 0.8931 (tptt) cc_final: 0.8327 (tppt)
REVERT: G   67 PHE cc_start: 0.8514 (t80) cc_final: 0.8254 (t80)
REVERT: G  100 MET cc_start: 0.7569 (tpp) cc_final: 0.7057 (tpp)
REVERT: G  108 LYS cc_start: 0.7620 (tmtt) cc_final: 0.6996 (tttt)
REVERT: G  120 ILE cc_start: 0.8857 (pt) cc_final: 0.8594 (mm)
REVERT: G  356 LEU cc_start: 0.7711 (pp) cc_final: 0.7377 (pp)
REVERT: A    9 LEU cc_start: 0.9262 (mt) cc_final: 0.8522 (mt)
REVERT: A   42 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8125 (mtmm)
REVERT: A   48 MET cc_start: 0.8115 (ttm) cc_final: 0.7418 (ttm)
REVERT: A   98 ASN cc_start: 0.8884 (t0) cc_final: 0.8544 (t0)
REVERT: A  107 ASP cc_start: 0.7729 (p0) cc_final: 0.7029 (m-30)
REVERT: A  108 ASP cc_start: 0.8702 (p0) cc_final: 0.8373 (p0)
REVERT: A  123 GLU cc_start: 0.8137 (pt0) cc_final: 0.7244 (tm-30)
REVERT: B   82 TYR cc_start: 0.8764 (t80) cc_final: 0.8195 (t80)
REVERT: B  100 MET cc_start: 0.7064 (mmm) cc_final: 0.6777 (mmm)
REVERT: B  122 MET cc_start: 0.8344 (mtm) cc_final: 0.7982 (mtm)
REVERT: B  126 HIS cc_start: 0.8028 (m-70) cc_final: 0.7509 (m170)
REVERT: B  145 ARG cc_start: 0.9080 (mtm-85) cc_final: 0.8475 (mtm180)
REVERT: B  162 ASP cc_start: 0.8803 (t0) cc_final: 0.8599 (t0)
REVERT: B  186 SER cc_start: 0.9045 (m) cc_final: 0.8684 (p)
REVERT: C    6 ARG cc_start: 0.6923 (mtp180) cc_final: 0.5992 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 306
  average time/residue: 0.0806
  time to fit residues: 33.9261
Evaluate side-chains
  248 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
F 319 ASN
A 136 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.144691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.120140 restraints weight = 12369.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.122649 restraints weight = 8122.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124398 restraints weight = 6096.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.125461 restraints weight = 5039.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.126117 restraints weight = 4453.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.5131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7406  Z= 0.129
  Angle     :  0.728  13.421  10023  Z= 0.350
  Chirality :  0.045   0.219   1205
  Planarity :  0.005   0.048   1246
  Dihedral  :  7.364  80.841   1050
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.28), residues: 911
  helix: -0.81 (0.25), residues: 459
  sheet: -1.57 (0.66), residues: 58
  loop : -2.04 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 133 
 TYR   0.031   0.001   TYR F  80 
 PHE   0.029   0.002   PHE G  67 
 TRP   0.008   0.001   TRP C   7 
 HIS   0.005   0.001   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7406)
  covalent geometry    : angle       0.72831 (10023)
  hydrogen bonds       : bond        0.03053 (  229)
  hydrogen bonds       : angle       4.59068 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5554 (tpp) cc_final: 0.5038 (ptt)
REVERT: F  282 MET cc_start: 0.9014 (ttp) cc_final: 0.8379 (tmm)
REVERT: G   20 MET cc_start: 0.6848 (tmm) cc_final: 0.6550 (tmm)
REVERT: G   28 SER cc_start: 0.8760 (m) cc_final: 0.8251 (t)
REVERT: G   62 LYS cc_start: 0.8972 (tptt) cc_final: 0.8310 (tppt)
REVERT: G   67 PHE cc_start: 0.8375 (t80) cc_final: 0.8111 (t80)
REVERT: G  100 MET cc_start: 0.7619 (tpp) cc_final: 0.7025 (tpp)
REVERT: G  108 LYS cc_start: 0.7543 (tmtt) cc_final: 0.6917 (tttt)
REVERT: G  120 ILE cc_start: 0.8882 (pt) cc_final: 0.8670 (mm)
REVERT: G  288 MET cc_start: 0.8510 (mmp) cc_final: 0.8308 (mmp)
REVERT: G  357 MET cc_start: 0.7602 (mmt) cc_final: 0.7364 (mmt)
REVERT: A    9 LEU cc_start: 0.9343 (mt) cc_final: 0.8864 (mp)
REVERT: A   42 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8187 (mtmm)
REVERT: A   48 MET cc_start: 0.8249 (ttm) cc_final: 0.7721 (ttm)
REVERT: A   98 ASN cc_start: 0.8943 (t0) cc_final: 0.8611 (t0)
REVERT: A  100 MET cc_start: 0.7995 (ttm) cc_final: 0.7721 (ttt)
REVERT: A  107 ASP cc_start: 0.7852 (p0) cc_final: 0.7044 (m-30)
REVERT: A  123 GLU cc_start: 0.8251 (pt0) cc_final: 0.7306 (tm-30)
REVERT: B    8 ASN cc_start: 0.8069 (m110) cc_final: 0.7176 (m-40)
REVERT: B   67 ILE cc_start: 0.9041 (pt) cc_final: 0.8715 (pt)
REVERT: B   82 TYR cc_start: 0.8858 (t80) cc_final: 0.8279 (t80)
REVERT: B  100 MET cc_start: 0.7306 (mmm) cc_final: 0.7071 (mmm)
REVERT: B  126 HIS cc_start: 0.8180 (m-70) cc_final: 0.7615 (m170)
REVERT: B  145 ARG cc_start: 0.9157 (mtm-85) cc_final: 0.8623 (mtm180)
REVERT: B  162 ASP cc_start: 0.8605 (t0) cc_final: 0.8388 (t0)
REVERT: B  186 SER cc_start: 0.9165 (m) cc_final: 0.8751 (p)
REVERT: C    6 ARG cc_start: 0.6877 (mtp180) cc_final: 0.5680 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.0760
  time to fit residues: 30.5214
Evaluate side-chains
  243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0040
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0070
   chunk 12 optimal weight:    0.0870
   chunk 29 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
G  85 GLN
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.147973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.123461 restraints weight = 12035.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.126039 restraints weight = 7924.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.127849 restraints weight = 5958.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.128701 restraints weight = 4932.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.129747 restraints weight = 4428.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7406  Z= 0.115
  Angle     :  0.726  13.026  10023  Z= 0.343
  Chirality :  0.044   0.233   1205
  Planarity :  0.005   0.048   1246
  Dihedral  :  7.180  78.948   1050
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.64 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.28), residues: 911
  helix: -0.60 (0.25), residues: 459
  sheet: -1.39 (0.67), residues: 58
  loop : -1.95 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  86 
 TYR   0.019   0.001   TYR B  96 
 PHE   0.029   0.001   PHE G  67 
 TRP   0.006   0.001   TRP F 330 
 HIS   0.003   0.000   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7406)
  covalent geometry    : angle       0.72565 (10023)
  hydrogen bonds       : bond        0.02773 (  229)
  hydrogen bonds       : angle       4.52342 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 283
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5387 (tpp) cc_final: 0.5035 (ptt)
REVERT: F   78 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7671 (tptt)
REVERT: G   20 MET cc_start: 0.6653 (tmm) cc_final: 0.6366 (tmm)
REVERT: G   28 SER cc_start: 0.8668 (m) cc_final: 0.8123 (t)
REVERT: G   62 LYS cc_start: 0.8949 (tptt) cc_final: 0.8367 (tppt)
REVERT: G  100 MET cc_start: 0.7481 (tpp) cc_final: 0.6932 (tpp)
REVERT: G  108 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7198 (tttt)
REVERT: G  118 MET cc_start: 0.7886 (mmt) cc_final: 0.7668 (mmt)
REVERT: G  120 ILE cc_start: 0.8787 (pt) cc_final: 0.8460 (mm)
REVERT: G  357 MET cc_start: 0.7633 (mmt) cc_final: 0.7425 (mmt)
REVERT: A    9 LEU cc_start: 0.9240 (mt) cc_final: 0.8484 (mt)
REVERT: A   42 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8120 (mtmm)
REVERT: A   48 MET cc_start: 0.8161 (ttm) cc_final: 0.7292 (ttm)
REVERT: A  107 ASP cc_start: 0.7642 (p0) cc_final: 0.7012 (m-30)
REVERT: A  108 ASP cc_start: 0.8712 (p0) cc_final: 0.8431 (p0)
REVERT: A  123 GLU cc_start: 0.8123 (pt0) cc_final: 0.7311 (tm-30)
REVERT: A  162 ASP cc_start: 0.9232 (t0) cc_final: 0.8957 (t0)
REVERT: A  194 ASP cc_start: 0.7505 (t0) cc_final: 0.7236 (t0)
REVERT: B   82 TYR cc_start: 0.8784 (t80) cc_final: 0.8216 (t80)
REVERT: B  100 MET cc_start: 0.6851 (mmm) cc_final: 0.6615 (mmm)
REVERT: B  119 ASN cc_start: 0.7717 (t0) cc_final: 0.7131 (t0)
REVERT: B  122 MET cc_start: 0.8223 (mtm) cc_final: 0.7962 (mtm)
REVERT: B  126 HIS cc_start: 0.7953 (m-70) cc_final: 0.7407 (m170)
REVERT: B  145 ARG cc_start: 0.9035 (mtm-85) cc_final: 0.8452 (mtm180)
REVERT: B  186 SER cc_start: 0.9100 (m) cc_final: 0.8768 (p)
REVERT: C    6 ARG cc_start: 0.6888 (mtp180) cc_final: 0.5931 (mtp-110)
  outliers start: 1
  outliers final: 0
  residues processed: 284
  average time/residue: 0.0845
  time to fit residues: 32.6211
Evaluate side-chains
  235 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0470
   chunk 2 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0370
   chunk 62 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.7758

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

Flipped N/Q/H residues before XYZ refinement:
G  85 GLN
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.144385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119111 restraints weight = 12317.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.121768 restraints weight = 7952.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123592 restraints weight = 5927.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.124833 restraints weight = 4861.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.125478 restraints weight = 4261.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.5413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7406  Z= 0.118
  Angle     :  0.719  12.464  10023  Z= 0.341
  Chirality :  0.044   0.235   1205
  Planarity :  0.005   0.048   1246
  Dihedral  :  7.144  76.395   1050
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.25 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.28), residues: 911
  helix: -0.48 (0.26), residues: 457
  sheet: -1.43 (0.68), residues: 58
  loop : -1.90 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 133 
 TYR   0.023   0.001   TYR F  80 
 PHE   0.029   0.001   PHE G  67 
 TRP   0.006   0.001   TRP F 330 
 HIS   0.003   0.000   HIS F  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7406)
  covalent geometry    : angle       0.71878 (10023)
  hydrogen bonds       : bond        0.02863 (  229)
  hydrogen bonds       : angle       4.46010 (  660)

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

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

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1822 Ramachandran restraints generated.
    911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 278
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5372 (tpp) cc_final: 0.5033 (ptt)
REVERT: F   78 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7665 (tptt)
REVERT: F  282 MET cc_start: 0.8760 (ttp) cc_final: 0.8147 (tmm)
REVERT: G   20 MET cc_start: 0.6673 (tmm) cc_final: 0.6344 (tmm)
REVERT: G   28 SER cc_start: 0.8701 (m) cc_final: 0.8124 (t)
REVERT: G   62 LYS cc_start: 0.8942 (tptt) cc_final: 0.8382 (tppt)
REVERT: G   82 MET cc_start: 0.7876 (ptt) cc_final: 0.7544 (ptp)
REVERT: G  100 MET cc_start: 0.7525 (tpp) cc_final: 0.7015 (tpp)
REVERT: G  108 LYS cc_start: 0.7667 (tmtt) cc_final: 0.7176 (tttt)
REVERT: G  120 ILE cc_start: 0.8791 (pt) cc_final: 0.8476 (mm)
REVERT: A    9 LEU cc_start: 0.9222 (mt) cc_final: 0.8745 (mp)
REVERT: A   42 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8111 (mtmm)
REVERT: A   48 MET cc_start: 0.8142 (ttm) cc_final: 0.7586 (ttm)
REVERT: A  107 ASP cc_start: 0.7643 (p0) cc_final: 0.6867 (m-30)
REVERT: A  123 GLU cc_start: 0.8273 (pt0) cc_final: 0.7531 (tm-30)
REVERT: A  194 ASP cc_start: 0.7509 (t0) cc_final: 0.7228 (t0)
REVERT: B    8 ASN cc_start: 0.8082 (m110) cc_final: 0.7343 (m110)
REVERT: B   82 TYR cc_start: 0.8747 (t80) cc_final: 0.8159 (t80)
REVERT: B   88 SER cc_start: 0.9366 (p) cc_final: 0.9020 (p)
REVERT: B  100 MET cc_start: 0.6822 (mmm) cc_final: 0.6589 (mmm)
REVERT: B  119 ASN cc_start: 0.7737 (t0) cc_final: 0.7160 (t0)
REVERT: B  122 MET cc_start: 0.8252 (mtm) cc_final: 0.7968 (mtm)
REVERT: B  126 HIS cc_start: 0.7930 (m-70) cc_final: 0.7415 (m170)
REVERT: B  145 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8487 (mtm180)
REVERT: B  186 SER cc_start: 0.9122 (m) cc_final: 0.8830 (p)
REVERT: C    6 ARG cc_start: 0.6913 (mtp180) cc_final: 0.5987 (mtp-110)
  outliers start: 1
  outliers final: 0
  residues processed: 279
  average time/residue: 0.0825
  time to fit residues: 31.2924
Evaluate side-chains
  235 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 88 optimal weight:    6.9990
   chunk 2 optimal weight:    0.3980
   chunk 58 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** 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 = 0.3602 r_free = 0.3602 target = 0.143693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.118434 restraints weight = 12467.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.121237 restraints weight = 7988.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.122922 restraints weight = 5894.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.124358 restraints weight = 4857.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.125084 restraints weight = 4237.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7406  Z= 0.116
  Angle     :  0.716  12.166  10023  Z= 0.341
  Chirality :  0.044   0.244   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  7.072  74.861   1050
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.28), residues: 911
  helix: -0.40 (0.26), residues: 457
  sheet: -1.38 (0.68), residues: 58
  loop : -1.88 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 144 
 TYR   0.021   0.001   TYR B  96 
 PHE   0.030   0.001   PHE G  67 
 TRP   0.006   0.001   TRP F 330 
 HIS   0.002   0.000   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7406)
  covalent geometry    : angle       0.71614 (10023)
  hydrogen bonds       : bond        0.02870 (  229)
  hydrogen bonds       : angle       4.48707 (  660)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1398.72 seconds
wall clock time: 24 minutes 44.88 seconds (1484.88 seconds total)