Starting phenix.real_space_refine
on Mon Apr 28 11:23:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mi7_9125/04_2025/6mi7_9125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mi7_9125/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mi7_9125/04_2025/6mi7_9125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mi7_9125/04_2025/6mi7_9125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mi7_9125/04_2025/6mi7_9125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mi7_9125/04_2025/6mi7_9125.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.87, per 1000 atoms: 0.67
  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: 1.52
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.80
  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: 1.63

  Time building geometry restraints manager: 1.85 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.990
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.920
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.014   0.002   TRP G 276 
 HIS   0.009   0.001   HIS F  89 
 PHE   0.039   0.003   PHE G  67 
 TYR   0.039   0.002   TYR F  80 
 ARG   0.005   0.001   ARG B 143 

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

*********************** 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  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    6 TYR cc_start: 0.9254 (t80) cc_final: 0.8526 (t80)
REVERT: F   59 MET cc_start: 0.5990 (tpp) cc_final: 0.5546 (ptt)
REVERT: F   78 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7678 (ttmt)
REVERT: F  281 LEU cc_start: 0.9068 (tt) cc_final: 0.8754 (tt)
REVERT: F  297 LEU cc_start: 0.9472 (tp) cc_final: 0.9220 (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: 0.9179 (t)
REVERT: G  100 MET cc_start: 0.7296 (tpp) cc_final: 0.6867 (tpp)
REVERT: G  108 LYS cc_start: 0.7410 (tmtt) cc_final: 0.6751 (tttt)
REVERT: G  254 LEU cc_start: 0.9044 (tp) cc_final: 0.8819 (mm)
REVERT: G  278 LYS cc_start: 0.9115 (ttmp) cc_final: 0.8823 (mtpt)
REVERT: G  351 ILE cc_start: 0.9169 (mt) cc_final: 0.8927 (mt)
REVERT: G  356 LEU cc_start: 0.7557 (pp) cc_final: 0.7350 (pp)
REVERT: A    8 ASN cc_start: 0.8481 (m110) cc_final: 0.8088 (m110)
REVERT: A   11 LYS cc_start: 0.8850 (tptp) cc_final: 0.8181 (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: 0.8336 (mm110)
REVERT: A  108 ASP cc_start: 0.9002 (p0) cc_final: 0.8694 (p0)
REVERT: A  116 ASP cc_start: 0.7986 (m-30) cc_final: 0.7681 (t0)
REVERT: A  123 GLU cc_start: 0.8180 (pt0) cc_final: 0.6570 (tm-30)
REVERT: A  128 GLU cc_start: 0.7529 (pm20) cc_final: 0.6903 (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: 0.8802 (t0)
REVERT: A  185 ASP cc_start: 0.8635 (t70) cc_final: 0.8208 (t0)
REVERT: A  220 THR cc_start: 0.7163 (p) cc_final: 0.6934 (m)
REVERT: B    8 ASN cc_start: 0.8517 (m110) cc_final: 0.7338 (m110)
REVERT: B   19 VAL cc_start: 0.9139 (t) cc_final: 0.8882 (t)
REVERT: B   44 THR cc_start: 0.8961 (m) cc_final: 0.8630 (m)
REVERT: B   82 TYR cc_start: 0.9066 (t80) cc_final: 0.8640 (t80)
REVERT: B   95 VAL cc_start: 0.9148 (t) cc_final: 0.8932 (p)
REVERT: B  100 MET cc_start: 0.8361 (mmm) cc_final: 0.7934 (mmm)
REVERT: B  113 GLN cc_start: 0.7647 (pm20) cc_final: 0.7362 (pm20)
REVERT: B  121 LEU cc_start: 0.9155 (tp) cc_final: 0.8821 (tt)
REVERT: B  126 HIS cc_start: 0.8155 (m-70) cc_final: 0.7483 (m170)
REVERT: B  145 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8545 (mtm180)
REVERT: B  169 ASP cc_start: 0.8616 (p0) cc_final: 0.8408 (p0)
REVERT: C    6 ARG cc_start: 0.7707 (mtp180) cc_final: 0.6003 (ptt180)
  outliers start: 3
  outliers final: 0
  residues processed: 374
  average time/residue: 0.2035
  time to fit residues: 98.5425
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  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.141447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.116428 restraints weight = 12247.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118813 restraints weight = 8168.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120578 restraints weight = 6211.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3242

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= 0.129
  Angle     :  0.734  11.124  10023  Z= 0.368
  Chirality :  0.044   0.239   1205
  Planarity :  0.005   0.049   1246
  Dihedral  :  9.167 116.916   1050
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  4.58 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.54 (0.23), residues: 911
  helix: -2.93 (0.19), residues: 453
  sheet: -3.09 (0.48), residues: 68
  loop : -2.94 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 330 
 HIS   0.003   0.001   HIS F  89 
 PHE   0.039   0.002   PHE G  67 
 TYR   0.021   0.001   TYR F  80 
 ARG   0.004   0.001   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04685 (  229)
  hydrogen bonds       : angle       6.01098 (  660)
  covalent geometry    : bond        0.00285 ( 7406)
  covalent geometry    : angle       0.73359 (10023)

*********************** 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
  341 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 339
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    5 ARG cc_start: 0.8313 (ttt-90) cc_final: 0.7932 (ttp80)
REVERT: F   59 MET cc_start: 0.5846 (tpp) cc_final: 0.5231 (ptt)
REVERT: F  279 MET cc_start: 0.8868 (mmp) cc_final: 0.8177 (mmp)
REVERT: G   20 MET cc_start: 0.6803 (tmm) cc_final: 0.6339 (tmm)
REVERT: G   85 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8570 (pp30)
REVERT: G  100 MET cc_start: 0.7140 (tpp) cc_final: 0.6856 (tpp)
REVERT: G  108 LYS cc_start: 0.7300 (tmtt) cc_final: 0.6902 (tttt)
REVERT: G  118 MET cc_start: 0.8032 (mmm) cc_final: 0.7825 (mmm)
REVERT: G  120 ILE cc_start: 0.8895 (pt) cc_final: 0.8482 (mm)
REVERT: G  356 LEU cc_start: 0.7828 (pp) cc_final: 0.7609 (pp)
REVERT: G  357 MET cc_start: 0.7656 (mmt) cc_final: 0.7397 (mmt)
REVERT: A    9 LEU cc_start: 0.9314 (mt) cc_final: 0.8975 (mp)
REVERT: A   98 ASN cc_start: 0.8635 (t0) cc_final: 0.8339 (t0)
REVERT: A  116 ASP cc_start: 0.7944 (m-30) cc_final: 0.7605 (t0)
REVERT: A  123 GLU cc_start: 0.8199 (pt0) cc_final: 0.6955 (tm-30)
REVERT: A  128 GLU cc_start: 0.7475 (pm20) cc_final: 0.6748 (pm20)
REVERT: A  155 ASN cc_start: 0.8062 (t0) cc_final: 0.7794 (t0)
REVERT: A  185 ASP cc_start: 0.8499 (t70) cc_final: 0.8250 (t0)
REVERT: A  220 THR cc_start: 0.7737 (p) cc_final: 0.5475 (p)
REVERT: B   67 ILE cc_start: 0.9290 (pt) cc_final: 0.9041 (pt)
REVERT: B   82 TYR cc_start: 0.8779 (t80) cc_final: 0.8326 (t80)
REVERT: B  126 HIS cc_start: 0.8170 (m-70) cc_final: 0.7105 (m170)
REVERT: B  145 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8431 (mtp85)
REVERT: B  169 ASP cc_start: 0.8805 (p0) cc_final: 0.8507 (p0)
REVERT: B  212 GLN cc_start: 0.9032 (mp10) cc_final: 0.8194 (mp10)
REVERT: B  231 LYS cc_start: 0.6773 (mmpt) cc_final: 0.6091 (pttm)
REVERT: C    6 ARG cc_start: 0.7469 (mtp180) cc_final: 0.6189 (ptt180)
REVERT: C   19 MET cc_start: 0.8093 (tpp) cc_final: 0.7758 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1720
  time to fit residues: 78.7256
Evaluate side-chains
  264 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 44 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0670
   chunk 36 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    2.1324

-------------------------------------------------------------------------------
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  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.135704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.110923 restraints weight = 12429.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113434 restraints weight = 8168.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114988 restraints weight = 6115.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7406  Z= 0.173
  Angle     :  0.737   9.886  10023  Z= 0.369
  Chirality :  0.046   0.220   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  8.707 100.885   1050
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.25), residues: 911
  helix: -2.21 (0.22), residues: 467
  sheet: -2.74 (0.51), residues: 68
  loop : -2.67 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 330 
 HIS   0.005   0.001   HIS F  89 
 PHE   0.033   0.002   PHE G  67 
 TYR   0.032   0.002   TYR F  80 
 ARG   0.004   0.001   ARG B 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  229)
  hydrogen bonds       : angle       5.56514 (  660)
  covalent geometry    : bond        0.00404 ( 7406)
  covalent geometry    : angle       0.73739 (10023)

*********************** 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
  300 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.6125 (tpp) cc_final: 0.5363 (ptt)
REVERT: F  282 MET cc_start: 0.9169 (ttp) cc_final: 0.8649 (tmm)
REVERT: F  297 LEU cc_start: 0.9469 (tp) cc_final: 0.9240 (tp)
REVERT: G   20 MET cc_start: 0.6902 (tmm) cc_final: 0.6480 (tmm)
REVERT: G   90 VAL cc_start: 0.9605 (p) cc_final: 0.9393 (t)
REVERT: G  100 MET cc_start: 0.7687 (tpp) cc_final: 0.7132 (tpp)
REVERT: G  108 LYS cc_start: 0.7516 (tmtt) cc_final: 0.7107 (tttt)
REVERT: G  120 ILE cc_start: 0.9010 (pt) cc_final: 0.8733 (mm)
REVERT: G  278 LYS cc_start: 0.9309 (mttt) cc_final: 0.9051 (mtpt)
REVERT: G  356 LEU cc_start: 0.7874 (pp) cc_final: 0.7611 (pp)
REVERT: G  357 MET cc_start: 0.7780 (mmt) cc_final: 0.7496 (mmt)
REVERT: A    9 LEU cc_start: 0.9442 (mt) cc_final: 0.9026 (mt)
REVERT: A   19 VAL cc_start: 0.9453 (t) cc_final: 0.9048 (t)
REVERT: A   98 ASN cc_start: 0.8853 (t0) cc_final: 0.8377 (t0)
REVERT: A  107 ASP cc_start: 0.7894 (p0) cc_final: 0.7187 (m-30)
REVERT: A  116 ASP cc_start: 0.8102 (m-30) cc_final: 0.7761 (t0)
REVERT: A  123 GLU cc_start: 0.8226 (pt0) cc_final: 0.7382 (tm-30)
REVERT: A  128 GLU cc_start: 0.7765 (pm20) cc_final: 0.6650 (pm20)
REVERT: A  155 ASN cc_start: 0.8269 (t0) cc_final: 0.8029 (t0)
REVERT: A  220 THR cc_start: 0.7374 (p) cc_final: 0.5866 (p)
REVERT: B    8 ASN cc_start: 0.8095 (m110) cc_final: 0.7218 (m110)
REVERT: B   82 TYR cc_start: 0.8872 (t80) cc_final: 0.8454 (t80)
REVERT: B  100 MET cc_start: 0.7909 (mmm) cc_final: 0.7522 (mmm)
REVERT: B  109 LEU cc_start: 0.6847 (mm) cc_final: 0.6605 (mm)
REVERT: B  122 MET cc_start: 0.8750 (mtt) cc_final: 0.8522 (mtm)
REVERT: B  126 HIS cc_start: 0.8283 (m-70) cc_final: 0.7573 (m170)
REVERT: B  128 GLU cc_start: 0.8146 (tp30) cc_final: 0.7704 (tm-30)
REVERT: B  145 ARG cc_start: 0.9201 (mtm-85) cc_final: 0.8580 (mtm180)
REVERT: B  169 ASP cc_start: 0.8822 (p0) cc_final: 0.8596 (p0)
REVERT: C    6 ARG cc_start: 0.7479 (mtp180) cc_final: 0.5964 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.1783
  time to fit residues: 71.7574
Evaluate side-chains
  249 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0970
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
F  15 GLN
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  27 ASN
** 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 = 0.3596 r_free = 0.3596 target = 0.143121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.118669 restraints weight = 12113.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121347 restraints weight = 7903.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.122988 restraints weight = 5889.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.4273

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= 0.115
  Angle     :  0.694  10.098  10023  Z= 0.340
  Chirality :  0.044   0.226   1205
  Planarity :  0.005   0.057   1246
  Dihedral  :  8.074  96.108   1050
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.69 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.26), residues: 911
  helix: -1.70 (0.23), residues: 458
  sheet: -2.25 (0.53), residues: 68
  loop : -2.49 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 330 
 HIS   0.002   0.000   HIS F  89 
 PHE   0.025   0.001   PHE G  67 
 TYR   0.022   0.001   TYR F  80 
 ARG   0.008   0.000   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  229)
  hydrogen bonds       : angle       5.02026 (  660)
  covalent geometry    : bond        0.00256 ( 7406)
  covalent geometry    : angle       0.69413 (10023)

*********************** 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: 1
    poor density    : 314
  time to evaluate  : 0.838 
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: 0.5203 (ptt)
REVERT: F   68 LEU cc_start: 0.9068 (tp) cc_final: 0.8814 (tt)
REVERT: F   78 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7556 (tptt)
REVERT: G   20 MET cc_start: 0.6927 (tmm) cc_final: 0.6510 (tmm)
REVERT: G   93 GLN cc_start: 0.9299 (tp40) cc_final: 0.8971 (tt0)
REVERT: G  100 MET cc_start: 0.7742 (tpp) cc_final: 0.7466 (tpp)
REVERT: G  108 LYS cc_start: 0.7565 (tmtt) cc_final: 0.6998 (tttt)
REVERT: G  120 ILE cc_start: 0.8947 (pt) cc_final: 0.8619 (mm)
REVERT: G  356 LEU cc_start: 0.7832 (pp) cc_final: 0.7386 (pp)
REVERT: A    9 LEU cc_start: 0.9310 (mt) cc_final: 0.9085 (mm)
REVERT: A   42 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8197 (mtmm)
REVERT: A  107 ASP cc_start: 0.7968 (p0) cc_final: 0.7271 (m-30)
REVERT: A  128 GLU cc_start: 0.7648 (pm20) cc_final: 0.7285 (pm20)
REVERT: A  155 ASN cc_start: 0.8253 (t0) cc_final: 0.8012 (t0)
REVERT: B   67 ILE cc_start: 0.9187 (pt) cc_final: 0.8918 (pt)
REVERT: B   82 TYR cc_start: 0.8762 (t80) cc_final: 0.8339 (t80)
REVERT: B   96 TYR cc_start: 0.8264 (t80) cc_final: 0.8046 (t80)
REVERT: B  100 MET cc_start: 0.7613 (mmm) cc_final: 0.7075 (mmm)
REVERT: B  126 HIS cc_start: 0.8278 (m-70) cc_final: 0.7769 (m170)
REVERT: B  145 ARG cc_start: 0.9211 (mtm-85) cc_final: 0.8632 (mtm180)
REVERT: B  147 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: B  162 ASP cc_start: 0.8735 (t0) cc_final: 0.8373 (t0)
REVERT: B  169 ASP cc_start: 0.8800 (p0) cc_final: 0.8549 (p0)
REVERT: B  186 SER cc_start: 0.9186 (m) cc_final: 0.8712 (p)
REVERT: C    6 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6296 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 314
  average time/residue: 0.1746
  time to fit residues: 74.2974
Evaluate side-chains
  250 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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**
A 212 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.133196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.107518 restraints weight = 12611.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.109889 restraints weight = 8320.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.111719 restraints weight = 6307.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7406  Z= 0.200
  Angle     :  0.775  10.204  10023  Z= 0.384
  Chirality :  0.048   0.219   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  8.311  87.256   1050
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.12 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.27), residues: 911
  helix: -1.53 (0.24), residues: 458
  sheet: -2.24 (0.54), residues: 68
  loop : -2.37 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 330 
 HIS   0.006   0.001   HIS F  89 
 PHE   0.041   0.002   PHE G  67 
 TYR   0.043   0.002   TYR F  80 
 ARG   0.004   0.001   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  229)
  hydrogen bonds       : angle       5.25671 (  660)
  covalent geometry    : bond        0.00476 ( 7406)
  covalent geometry    : angle       0.77488 (10023)

*********************** 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
  287 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.843 
Fit side-chains
REVERT: F   59 MET cc_start: 0.6171 (tpp) cc_final: 0.5487 (ptt)
REVERT: F   86 THR cc_start: 0.9341 (m) cc_final: 0.9049 (m)
REVERT: F  282 MET cc_start: 0.8543 (tmm) cc_final: 0.8262 (tmm)
REVERT: G    8 ASP cc_start: 0.7834 (p0) cc_final: 0.7571 (p0)
REVERT: G    9 ARG cc_start: 0.6773 (mpt180) cc_final: 0.6258 (ttm110)
REVERT: G   20 MET cc_start: 0.6963 (tmm) cc_final: 0.6604 (tmm)
REVERT: G  100 MET cc_start: 0.7872 (tpp) cc_final: 0.7548 (tpp)
REVERT: G  108 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7236 (tttt)
REVERT: G  115 LEU cc_start: 0.8819 (mt) cc_final: 0.8556 (pp)
REVERT: G  120 ILE cc_start: 0.8958 (pt) cc_final: 0.8715 (mm)
REVERT: G  278 LYS cc_start: 0.9365 (mtmt) cc_final: 0.9129 (mtpt)
REVERT: A    9 LEU cc_start: 0.9406 (mt) cc_final: 0.9099 (mt)
REVERT: A   17 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7389 (ttm110)
REVERT: A   42 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8354 (mtmm)
REVERT: A   48 MET cc_start: 0.8214 (ttm) cc_final: 0.7961 (ttm)
REVERT: A  107 ASP cc_start: 0.8020 (p0) cc_final: 0.7373 (m-30)
REVERT: A  128 GLU cc_start: 0.7467 (pm20) cc_final: 0.7264 (pm20)
REVERT: A  150 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8653 (tmm-80)
REVERT: A  162 ASP cc_start: 0.8946 (t70) cc_final: 0.8528 (t0)
REVERT: B    8 ASN cc_start: 0.8020 (m110) cc_final: 0.6959 (m-40)
REVERT: B   67 ILE cc_start: 0.9238 (pt) cc_final: 0.8933 (pt)
REVERT: B   82 TYR cc_start: 0.8836 (t80) cc_final: 0.8369 (t80)
REVERT: B   96 TYR cc_start: 0.8375 (t80) cc_final: 0.8174 (t80)
REVERT: B  100 MET cc_start: 0.7547 (mmm) cc_final: 0.7150 (mmm)
REVERT: B  126 HIS cc_start: 0.8229 (m-70) cc_final: 0.7615 (m170)
REVERT: B  145 ARG cc_start: 0.9133 (mtm-85) cc_final: 0.8728 (mtm180)
REVERT: B  186 SER cc_start: 0.9228 (m) cc_final: 0.8726 (p)
REVERT: C    6 ARG cc_start: 0.7680 (mtp180) cc_final: 0.6533 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.1949
  time to fit residues: 74.7283
Evaluate side-chains
  240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0060
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.7200

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.137883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.112164 restraints weight = 12568.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.114610 restraints weight = 8246.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.116564 restraints weight = 6227.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4783

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= 0.115
  Angle     :  0.704  12.211  10023  Z= 0.340
  Chirality :  0.044   0.236   1205
  Planarity :  0.004   0.047   1246
  Dihedral  :  7.821  84.100   1050
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.27), residues: 911
  helix: -1.31 (0.24), residues: 466
  sheet: -2.11 (0.59), residues: 58
  loop : -2.16 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 330 
 HIS   0.002   0.000   HIS A  73 
 PHE   0.028   0.002   PHE G  67 
 TYR   0.024   0.001   TYR F  80 
 ARG   0.003   0.000   ARG G 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  229)
  hydrogen bonds       : angle       4.93084 (  660)
  covalent geometry    : bond        0.00259 ( 7406)
  covalent geometry    : angle       0.70387 (10023)

*********************** 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
  288 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5936 (tpp) cc_final: 0.5364 (ptt)
REVERT: F   72 LEU cc_start: 0.9428 (tp) cc_final: 0.9224 (tp)
REVERT: F  105 LEU cc_start: 0.9127 (pp) cc_final: 0.8912 (pp)
REVERT: F  282 MET cc_start: 0.8504 (tmm) cc_final: 0.8124 (tmm)
REVERT: G    8 ASP cc_start: 0.7767 (p0) cc_final: 0.7533 (p0)
REVERT: G    9 ARG cc_start: 0.6594 (mpt180) cc_final: 0.6169 (ttm110)
REVERT: G   20 MET cc_start: 0.6988 (tmm) cc_final: 0.6666 (tmm)
REVERT: G  100 MET cc_start: 0.7657 (tpp) cc_final: 0.7311 (tpp)
REVERT: G  108 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7355 (tttt)
REVERT: G  120 ILE cc_start: 0.8856 (pt) cc_final: 0.8614 (mm)
REVERT: G  356 LEU cc_start: 0.7966 (pp) cc_final: 0.7762 (pp)
REVERT: G  357 MET cc_start: 0.7849 (mmt) cc_final: 0.7569 (mmt)
REVERT: A   42 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8293 (mtmm)
REVERT: A  107 ASP cc_start: 0.7956 (p0) cc_final: 0.7324 (m-30)
REVERT: A  108 ASP cc_start: 0.8764 (p0) cc_final: 0.8396 (p0)
REVERT: A  162 ASP cc_start: 0.8927 (t70) cc_final: 0.8487 (t0)
REVERT: A  194 ASP cc_start: 0.7700 (t0) cc_final: 0.7445 (t0)
REVERT: B   82 TYR cc_start: 0.8757 (t80) cc_final: 0.8275 (t80)
REVERT: B   97 ASP cc_start: 0.7804 (m-30) cc_final: 0.7342 (m-30)
REVERT: B  100 MET cc_start: 0.7298 (mmm) cc_final: 0.6899 (mmm)
REVERT: B  126 HIS cc_start: 0.8188 (m-70) cc_final: 0.7560 (m170)
REVERT: B  145 ARG cc_start: 0.9113 (mtm-85) cc_final: 0.8754 (mtm180)
REVERT: B  163 GLU cc_start: 0.8601 (mp0) cc_final: 0.8345 (mp0)
REVERT: B  186 SER cc_start: 0.9185 (m) cc_final: 0.8724 (p)
REVERT: C    6 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6362 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.1747
  time to fit residues: 67.5827
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  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0170
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7418

-------------------------------------------------------------------------------
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 = 0.3565 r_free = 0.3565 target = 0.140365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.115460 restraints weight = 12289.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118010 restraints weight = 8321.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.119717 restraints weight = 6300.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.4967

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= 0.118
  Angle     :  0.716  12.420  10023  Z= 0.345
  Chirality :  0.044   0.238   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  7.694  81.710   1050
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.27), residues: 911
  helix: -1.10 (0.24), residues: 461
  sheet: -1.94 (0.56), residues: 68
  loop : -2.13 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 268 
 HIS   0.004   0.001   HIS F  89 
 PHE   0.061   0.002   PHE G  67 
 TYR   0.021   0.001   TYR B  13 
 ARG   0.003   0.000   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03150 (  229)
  hydrogen bonds       : angle       4.87112 (  660)
  covalent geometry    : bond        0.00268 ( 7406)
  covalent geometry    : angle       0.71615 (10023)

*********************** 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
  308 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5827 (tpp) cc_final: 0.5112 (ptt)
REVERT: F   72 LEU cc_start: 0.9386 (tp) cc_final: 0.9013 (tt)
REVERT: F  105 LEU cc_start: 0.9092 (pp) cc_final: 0.8858 (pp)
REVERT: G    9 ARG cc_start: 0.7090 (mpt180) cc_final: 0.6540 (ttm110)
REVERT: G   20 MET cc_start: 0.6961 (tmm) cc_final: 0.6525 (tmm)
REVERT: G   28 SER cc_start: 0.8781 (m) cc_final: 0.8235 (t)
REVERT: G   62 LYS cc_start: 0.9218 (tptt) cc_final: 0.8852 (tppt)
REVERT: G  100 MET cc_start: 0.7651 (tpp) cc_final: 0.7131 (tpp)
REVERT: G  108 LYS cc_start: 0.7927 (tmtt) cc_final: 0.7276 (tttt)
REVERT: G  357 MET cc_start: 0.7894 (mmt) cc_final: 0.7606 (mmt)
REVERT: A   42 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8361 (mtmm)
REVERT: A  107 ASP cc_start: 0.8049 (p0) cc_final: 0.7306 (m-30)
REVERT: A  108 ASP cc_start: 0.8778 (p0) cc_final: 0.8428 (p0)
REVERT: A  162 ASP cc_start: 0.8962 (t70) cc_final: 0.8438 (t0)
REVERT: B    8 ASN cc_start: 0.8134 (m110) cc_final: 0.6998 (m-40)
REVERT: B   82 TYR cc_start: 0.8892 (t80) cc_final: 0.8418 (t80)
REVERT: B  100 MET cc_start: 0.7336 (mmm) cc_final: 0.7013 (mmm)
REVERT: B  126 HIS cc_start: 0.8224 (m-70) cc_final: 0.7670 (m170)
REVERT: B  145 ARG cc_start: 0.9149 (mtm-85) cc_final: 0.8803 (mtm180)
REVERT: B  183 LEU cc_start: 0.9229 (pp) cc_final: 0.9019 (tt)
REVERT: B  186 SER cc_start: 0.9175 (m) cc_final: 0.8793 (p)
REVERT: C    6 ARG cc_start: 0.6900 (mtp180) cc_final: 0.6300 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.1656
  time to fit residues: 69.8174
Evaluate side-chains
  251 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 59 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    0.3980
   chunk 61 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.138757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114017 restraints weight = 12478.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.116527 restraints weight = 8291.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.118293 restraints weight = 6301.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.5144

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= 0.126
  Angle     :  0.749  14.426  10023  Z= 0.357
  Chirality :  0.045   0.237   1205
  Planarity :  0.005   0.064   1246
  Dihedral  :  7.580  79.705   1050
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.28), residues: 911
  helix: -1.02 (0.25), residues: 463
  sheet: -1.82 (0.62), residues: 58
  loop : -1.99 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 330 
 HIS   0.003   0.001   HIS F  89 
 PHE   0.051   0.002   PHE G  67 
 TYR   0.018   0.001   TYR B  96 
 ARG   0.012   0.000   ARG B  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  229)
  hydrogen bonds       : angle       4.78760 (  660)
  covalent geometry    : bond        0.00292 ( 7406)
  covalent geometry    : angle       0.74928 (10023)

*********************** 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
  285 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5747 (tpp) cc_final: 0.5308 (ptt)
REVERT: F   72 LEU cc_start: 0.9463 (tp) cc_final: 0.9137 (tp)
REVERT: G   20 MET cc_start: 0.6954 (tmm) cc_final: 0.6516 (tmm)
REVERT: G   28 SER cc_start: 0.8871 (m) cc_final: 0.8250 (t)
REVERT: G   62 LYS cc_start: 0.9228 (tptt) cc_final: 0.8940 (tppt)
REVERT: G  100 MET cc_start: 0.7459 (tpp) cc_final: 0.6965 (tpp)
REVERT: G  108 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7587 (tttt)
REVERT: A    9 LEU cc_start: 0.8636 (mm) cc_final: 0.8157 (mt)
REVERT: A   42 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8355 (mtmm)
REVERT: A  107 ASP cc_start: 0.7855 (p0) cc_final: 0.7075 (m-30)
REVERT: A  162 ASP cc_start: 0.8865 (t70) cc_final: 0.8590 (t0)
REVERT: A  194 ASP cc_start: 0.7562 (t0) cc_final: 0.7332 (t0)
REVERT: B   61 ILE cc_start: 0.9093 (pt) cc_final: 0.8764 (mm)
REVERT: B   82 TYR cc_start: 0.8803 (t80) cc_final: 0.8231 (t80)
REVERT: B   88 SER cc_start: 0.9336 (p) cc_final: 0.9017 (p)
REVERT: B  100 MET cc_start: 0.7186 (mmm) cc_final: 0.6920 (mmm)
REVERT: B  126 HIS cc_start: 0.8027 (m-70) cc_final: 0.7432 (m170)
REVERT: B  145 ARG cc_start: 0.9096 (mtm-85) cc_final: 0.8793 (mtm180)
REVERT: B  183 LEU cc_start: 0.9261 (pp) cc_final: 0.9023 (tt)
REVERT: B  186 SER cc_start: 0.9148 (m) cc_final: 0.8749 (p)
REVERT: C    6 ARG cc_start: 0.6998 (mtp180) cc_final: 0.6359 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.1750
  time to fit residues: 67.7468
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  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0070
   chunk 2 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.5802

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

Flipped N/Q/H residues before XYZ refinement:
F 128 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 = 0.3582 r_free = 0.3582 target = 0.141720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.117461 restraints weight = 12438.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119986 restraints weight = 8174.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.121816 restraints weight = 6139.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7406  Z= 0.148
  Angle     :  0.767  12.060  10023  Z= 0.371
  Chirality :  0.046   0.235   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  7.645  77.526   1050
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.28), residues: 911
  helix: -0.99 (0.25), residues: 465
  sheet: -1.71 (0.64), residues: 58
  loop : -1.94 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 330 
 HIS   0.006   0.001   HIS F  89 
 PHE   0.053   0.002   PHE G  67 
 TYR   0.031   0.002   TYR F  80 
 ARG   0.004   0.000   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  229)
  hydrogen bonds       : angle       4.84297 (  660)
  covalent geometry    : bond        0.00349 ( 7406)
  covalent geometry    : angle       0.76699 (10023)

*********************** 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
  290 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: F   26 PHE cc_start: 0.7727 (m-10) cc_final: 0.7451 (m-10)
REVERT: F   59 MET cc_start: 0.5764 (tpp) cc_final: 0.5263 (ptt)
REVERT: F   72 LEU cc_start: 0.9353 (tp) cc_final: 0.9088 (tt)
REVERT: F  105 LEU cc_start: 0.9148 (pp) cc_final: 0.8897 (pp)
REVERT: F  282 MET cc_start: 0.8657 (tmm) cc_final: 0.8350 (tmm)
REVERT: G   20 MET cc_start: 0.6920 (tmm) cc_final: 0.6571 (tmm)
REVERT: G   62 LYS cc_start: 0.9220 (tptt) cc_final: 0.8895 (tppt)
REVERT: G  100 MET cc_start: 0.7540 (tpp) cc_final: 0.7005 (tpp)
REVERT: G  108 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7526 (tttt)
REVERT: G  288 MET cc_start: 0.8427 (mmp) cc_final: 0.8185 (mmp)
REVERT: A   42 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8427 (mtmm)
REVERT: A  107 ASP cc_start: 0.7941 (p0) cc_final: 0.7320 (m-30)
REVERT: A  108 ASP cc_start: 0.8693 (p0) cc_final: 0.8387 (p0)
REVERT: A  162 ASP cc_start: 0.9037 (t70) cc_final: 0.8544 (t0)
REVERT: A  194 ASP cc_start: 0.7683 (t0) cc_final: 0.7382 (t0)
REVERT: B    8 ASN cc_start: 0.8066 (m110) cc_final: 0.7128 (m110)
REVERT: B   19 VAL cc_start: 0.9165 (t) cc_final: 0.8885 (t)
REVERT: B   61 ILE cc_start: 0.9142 (pt) cc_final: 0.8856 (mm)
REVERT: B   82 TYR cc_start: 0.8805 (t80) cc_final: 0.8255 (t80)
REVERT: B  100 MET cc_start: 0.7459 (mmm) cc_final: 0.7184 (mmm)
REVERT: B  126 HIS cc_start: 0.8107 (m-70) cc_final: 0.7559 (m170)
REVERT: B  186 SER cc_start: 0.9202 (m) cc_final: 0.8824 (p)
REVERT: C    6 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6439 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1653
  time to fit residues: 65.2445
Evaluate side-chains
  238 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 14 optimal weight:    0.0070
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0050
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 80 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.6814

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

Flipped N/Q/H residues before XYZ refinement:
A 136 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 = 0.3606 r_free = 0.3606 target = 0.143902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119290 restraints weight = 12494.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.122010 restraints weight = 8058.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.123629 restraints weight = 5968.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5408

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= 0.122
  Angle     :  0.755  13.146  10023  Z= 0.360
  Chirality :  0.045   0.239   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.434  76.444   1050
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.28), residues: 911
  helix: -0.83 (0.25), residues: 463
  sheet: -1.65 (0.65), residues: 58
  loop : -1.94 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 268 
 HIS   0.003   0.001   HIS F  89 
 PHE   0.029   0.002   PHE G  67 
 TYR   0.020   0.001   TYR B  96 
 ARG   0.004   0.000   ARG G 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  229)
  hydrogen bonds       : angle       4.77127 (  660)
  covalent geometry    : bond        0.00277 ( 7406)
  covalent geometry    : angle       0.75523 (10023)

********************** 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
  278 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5676 (tpp) cc_final: 0.5162 (ptt)
REVERT: F   72 LEU cc_start: 0.9419 (tp) cc_final: 0.9065 (tp)
REVERT: F  105 LEU cc_start: 0.9096 (pp) cc_final: 0.8873 (pp)
REVERT: G   20 MET cc_start: 0.6988 (tmm) cc_final: 0.6626 (tmm)
REVERT: G   28 SER cc_start: 0.8798 (m) cc_final: 0.8259 (t)
REVERT: G   62 LYS cc_start: 0.9176 (tptt) cc_final: 0.8891 (tppt)
REVERT: G  100 MET cc_start: 0.7524 (tpp) cc_final: 0.7017 (tpp)
REVERT: G  108 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7547 (tttt)
REVERT: A   42 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8397 (mtmm)
REVERT: A  107 ASP cc_start: 0.7846 (p0) cc_final: 0.7280 (m-30)
REVERT: A  108 ASP cc_start: 0.8696 (p0) cc_final: 0.8424 (p0)
REVERT: A  162 ASP cc_start: 0.9000 (t70) cc_final: 0.8487 (t0)
REVERT: A  194 ASP cc_start: 0.7580 (t0) cc_final: 0.7270 (t0)
REVERT: B   82 TYR cc_start: 0.8792 (t80) cc_final: 0.8289 (t80)
REVERT: B  100 MET cc_start: 0.7297 (mmm) cc_final: 0.6964 (mmm)
REVERT: B  122 MET cc_start: 0.8615 (mtm) cc_final: 0.8385 (mpp)
REVERT: B  126 HIS cc_start: 0.8064 (m-70) cc_final: 0.7563 (m170)
REVERT: B  186 SER cc_start: 0.9179 (m) cc_final: 0.8746 (p)
REVERT: C    6 ARG cc_start: 0.6994 (mtp180) cc_final: 0.6295 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.1573
  time to fit residues: 60.1974
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  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    0.2980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.116454 restraints weight = 12314.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.119132 restraints weight = 8000.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.120931 restraints weight = 5950.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.5477

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= 0.122
  Angle     :  0.748  13.346  10023  Z= 0.357
  Chirality :  0.045   0.217   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.340  75.148   1050
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.28), residues: 911
  helix: -0.73 (0.25), residues: 465
  sheet: -1.51 (0.66), residues: 58
  loop : -1.96 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 268 
 HIS   0.003   0.001   HIS F  89 
 PHE   0.028   0.001   PHE G  67 
 TYR   0.021   0.001   TYR B  13 
 ARG   0.003   0.000   ARG G 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03095 (  229)
  hydrogen bonds       : angle       4.70211 (  660)
  covalent geometry    : bond        0.00279 ( 7406)
  covalent geometry    : angle       0.74840 (10023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2652.90 seconds
wall clock time: 46 minutes 26.15 seconds (2786.15 seconds total)