Starting phenix.real_space_refine
on Wed Feb 12 06:49:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mi7_9125/02_2025/6mi7_9125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mi7_9125/02_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_9125/02_2025/6mi7_9125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mi7_9125/02_2025/6mi7_9125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mi7_9125/02_2025/6mi7_9125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mi7_9125/02_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-5592/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: 4.64, per 1000 atoms: 0.64
  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: 1.92
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.72
  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: 1.94

  Time building geometry restraints manager: 2.11 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 62
        2.62 -     3.19: 6058
        3.19 -     3.76: 10728
        3.76 -     4.33: 14294
        4.33 -     4.90: 22444
  Nonbonded interactions: 53586
  Sorted by model distance:
  nonbonded pdb=" O1P PGT F 401 "
            pdb=" O5  PGT F 401 "
     model   vdw
     2.053 3.040
  nonbonded pdb=" OG1 THR A 220 "
            pdb=" OE1 GLU A 223 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR A  96 "
            pdb=" OE1 GLU A 115 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   SER A  88 "
            pdb=" NH2 ARG A 150 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OE2 GLU F  82 "
            pdb=" NH1 ARG B  91 "
     model   vdw
     2.353 3.120
  ... (remaining 53581 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.080
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.800
-------------------------------------------------------------------------------
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= 0.362
  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 

*********************** 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  : 0.805 
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: 0.2064
  time to fit residues: 99.4994
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  : 0.827 
-------------------------------------------------------------------------------
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 = 0.3568 r_free = 0.3568 target = 0.141140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.116157 restraints weight = 12263.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.118588 restraints weight = 8171.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.120134 restraints weight = 6202.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
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= 0.185
  Angle     :  0.734  11.122  10023  Z= 0.368
  Chirality :  0.044   0.239   1205
  Planarity :  0.005   0.049   1246
  Dihedral  :  9.167 116.917   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 

*********************** 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  : 0.859 
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: 0.5852 (tpp) cc_final: 0.5230 (ptt)
REVERT: F  279 MET cc_start: 0.8870 (mmp) cc_final: 0.8179 (mmp)
REVERT: G   20 MET cc_start: 0.6800 (tmm) cc_final: 0.6334 (tmm)
REVERT: G   85 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8568 (pp30)
REVERT: G  100 MET cc_start: 0.7134 (tpp) cc_final: 0.6849 (tpp)
REVERT: G  108 LYS cc_start: 0.7297 (tmtt) cc_final: 0.6900 (tttt)
REVERT: G  118 MET cc_start: 0.8034 (mmm) cc_final: 0.7827 (mmm)
REVERT: G  120 ILE cc_start: 0.8895 (pt) cc_final: 0.8479 (mm)
REVERT: G  356 LEU cc_start: 0.7827 (pp) cc_final: 0.7608 (pp)
REVERT: G  357 MET cc_start: 0.7665 (mmt) cc_final: 0.7405 (mmt)
REVERT: A    9 LEU cc_start: 0.9310 (mt) cc_final: 0.8971 (mp)
REVERT: A   98 ASN cc_start: 0.8631 (t0) cc_final: 0.8339 (t0)
REVERT: A  116 ASP cc_start: 0.7960 (m-30) cc_final: 0.7611 (t0)
REVERT: A  123 GLU cc_start: 0.8210 (pt0) cc_final: 0.6955 (tm-30)
REVERT: A  128 GLU cc_start: 0.7485 (pm20) cc_final: 0.6742 (pm20)
REVERT: A  155 ASN cc_start: 0.8061 (t0) cc_final: 0.7794 (t0)
REVERT: A  185 ASP cc_start: 0.8505 (t70) cc_final: 0.8253 (t0)
REVERT: A  220 THR cc_start: 0.7746 (p) cc_final: 0.5500 (p)
REVERT: B   67 ILE cc_start: 0.9296 (pt) cc_final: 0.9036 (pt)
REVERT: B   82 TYR cc_start: 0.8780 (t80) cc_final: 0.8325 (t80)
REVERT: B  126 HIS cc_start: 0.8184 (m-70) cc_final: 0.7118 (m170)
REVERT: B  145 ARG cc_start: 0.9082 (mtm-85) cc_final: 0.8431 (mtp85)
REVERT: B  169 ASP cc_start: 0.8808 (p0) cc_final: 0.8511 (p0)
REVERT: B  212 GLN cc_start: 0.9031 (mp10) cc_final: 0.8194 (mp10)
REVERT: B  231 LYS cc_start: 0.6776 (mmpt) cc_final: 0.6089 (pttm)
REVERT: C    6 ARG cc_start: 0.7472 (mtp180) cc_final: 0.6183 (ptt180)
REVERT: C   19 MET cc_start: 0.8098 (tpp) cc_final: 0.7759 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1810
  time to fit residues: 82.8051
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  : 0.873 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.134664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.110241 restraints weight = 12578.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.112629 restraints weight = 8429.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.114101 restraints weight = 6378.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   7406  Z= 0.401
  Angle     :  0.827   9.336  10023  Z= 0.419
  Chirality :  0.049   0.214   1205
  Planarity :  0.006   0.046   1246
  Dihedral  :  9.016  98.416   1050
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.23 %
    Favored  : 93.64 %
  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: -3.85 (0.25), residues: 911
  helix: -2.29 (0.22), residues: 461
  sheet: -2.91 (0.49), residues: 68
  loop : -2.67 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 330 
 HIS   0.009   0.001   HIS F  89 
 PHE   0.037   0.003   PHE G  67 
 TYR   0.033   0.002   TYR F  80 
 ARG   0.005   0.001   ARG B 106 

*********************** 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
  292 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 291
  time to evaluate  : 0.824 
Fit side-chains
REVERT: F   59 MET cc_start: 0.6412 (tpp) cc_final: 0.5835 (ptt)
REVERT: F  282 MET cc_start: 0.9203 (ttp) cc_final: 0.8604 (tmm)
REVERT: F  297 LEU cc_start: 0.9545 (tp) cc_final: 0.9273 (tp)
REVERT: G   20 MET cc_start: 0.6905 (tmm) cc_final: 0.6524 (tmm)
REVERT: G  100 MET cc_start: 0.7866 (tpp) cc_final: 0.7278 (tpp)
REVERT: G  108 LYS cc_start: 0.7473 (tmtt) cc_final: 0.6976 (tttt)
REVERT: G  120 ILE cc_start: 0.9070 (pt) cc_final: 0.8800 (mm)
REVERT: G  278 LYS cc_start: 0.9326 (mttt) cc_final: 0.8919 (mtpt)
REVERT: G  356 LEU cc_start: 0.7946 (pp) cc_final: 0.7646 (pp)
REVERT: G  357 MET cc_start: 0.7842 (mmt) cc_final: 0.7572 (mmt)
REVERT: A    9 LEU cc_start: 0.9486 (mt) cc_final: 0.9166 (mt)
REVERT: A   19 VAL cc_start: 0.9443 (t) cc_final: 0.9046 (t)
REVERT: A   48 MET cc_start: 0.8339 (ttm) cc_final: 0.8127 (ttm)
REVERT: A   98 ASN cc_start: 0.8989 (t0) cc_final: 0.8439 (t0)
REVERT: A  107 ASP cc_start: 0.7966 (p0) cc_final: 0.7276 (m-30)
REVERT: A  123 GLU cc_start: 0.8183 (pt0) cc_final: 0.7421 (tm-30)
REVERT: A  128 GLU cc_start: 0.7833 (pm20) cc_final: 0.6812 (pm20)
REVERT: A  155 ASN cc_start: 0.8285 (t0) cc_final: 0.8056 (t0)
REVERT: A  218 HIS cc_start: 0.8866 (p-80) cc_final: 0.8650 (p-80)
REVERT: A  220 THR cc_start: 0.7442 (p) cc_final: 0.5832 (p)
REVERT: B    8 ASN cc_start: 0.8089 (m110) cc_final: 0.7196 (m110)
REVERT: B   61 ILE cc_start: 0.9192 (pt) cc_final: 0.8875 (mm)
REVERT: B   67 ILE cc_start: 0.9271 (pt) cc_final: 0.9005 (pt)
REVERT: B   68 SER cc_start: 0.8899 (m) cc_final: 0.8676 (p)
REVERT: B   82 TYR cc_start: 0.8939 (t80) cc_final: 0.8484 (t80)
REVERT: B  126 HIS cc_start: 0.8278 (m-70) cc_final: 0.7551 (m170)
REVERT: B  145 ARG cc_start: 0.9206 (mtm-85) cc_final: 0.8560 (mtm180)
REVERT: B  169 ASP cc_start: 0.8790 (p0) cc_final: 0.8587 (p0)
REVERT: B  196 ASN cc_start: 0.8600 (t0) cc_final: 0.8212 (t0)
REVERT: C    6 ARG cc_start: 0.7747 (mtp180) cc_final: 0.5957 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 292
  average time/residue: 0.1811
  time to fit residues: 69.9495
Evaluate side-chains
  248 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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**
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.139597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.115290 restraints weight = 12302.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.117923 restraints weight = 8020.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.119666 restraints weight = 5955.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4316

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= 0.174
  Angle     :  0.708  11.443  10023  Z= 0.348
  Chirality :  0.045   0.224   1205
  Planarity :  0.005   0.050   1246
  Dihedral  :  8.183  92.668   1050
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  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: -3.33 (0.26), residues: 911
  helix: -1.84 (0.23), residues: 468
  sheet: -2.48 (0.50), residues: 68
  loop : -2.50 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 330 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.043   0.002   PHE G  67 
 TYR   0.024   0.001   TYR F  80 
 ARG   0.004   0.000   ARG B 150 

*********************** 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
  304 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   13 LYS cc_start: 0.8249 (tttt) cc_final: 0.7677 (ttmt)
REVERT: F   59 MET cc_start: 0.5959 (tpp) cc_final: 0.5315 (ptt)
REVERT: F   78 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7613 (tptt)
REVERT: F  282 MET cc_start: 0.8634 (tmm) cc_final: 0.8072 (tmm)
REVERT: F  297 LEU cc_start: 0.9372 (tp) cc_final: 0.9137 (tp)
REVERT: G   20 MET cc_start: 0.6825 (tmm) cc_final: 0.6442 (tmm)
REVERT: G  100 MET cc_start: 0.7865 (tpp) cc_final: 0.7441 (tpp)
REVERT: G  108 LYS cc_start: 0.7594 (tmtt) cc_final: 0.7034 (tttt)
REVERT: G  120 ILE cc_start: 0.8978 (pt) cc_final: 0.8695 (mm)
REVERT: G  356 LEU cc_start: 0.7804 (pp) cc_final: 0.7380 (pp)
REVERT: A    9 LEU cc_start: 0.9418 (mt) cc_final: 0.9212 (mt)
REVERT: A   42 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8293 (mtmm)
REVERT: A   98 ASN cc_start: 0.8790 (t0) cc_final: 0.8383 (t0)
REVERT: A  107 ASP cc_start: 0.7821 (p0) cc_final: 0.7170 (m-30)
REVERT: A  128 GLU cc_start: 0.7606 (pm20) cc_final: 0.7378 (pm20)
REVERT: A  155 ASN cc_start: 0.8140 (t0) cc_final: 0.7920 (t0)
REVERT: B   68 SER cc_start: 0.9006 (m) cc_final: 0.8481 (p)
REVERT: B   82 TYR cc_start: 0.8745 (t80) cc_final: 0.8339 (t80)
REVERT: B  126 HIS cc_start: 0.8241 (m-70) cc_final: 0.7633 (m170)
REVERT: B  145 ARG cc_start: 0.9195 (mtm-85) cc_final: 0.8648 (mtm180)
REVERT: B  147 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8079 (mt-10)
REVERT: B  169 ASP cc_start: 0.8710 (p0) cc_final: 0.8487 (p0)
REVERT: C    6 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6400 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1872
  time to fit residues: 76.9489
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  : 0.935 
-------------------------------------------------------------------------------
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:    0.0010
   chunk 67 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.4586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.140203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.115684 restraints weight = 12427.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118204 restraints weight = 8363.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.119768 restraints weight = 6292.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7406  Z= 0.161
  Angle     :  0.687  13.392  10023  Z= 0.330
  Chirality :  0.044   0.235   1205
  Planarity :  0.004   0.047   1246
  Dihedral  :  7.808  88.285   1050
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.82 (0.27), residues: 911
  helix: -1.42 (0.24), residues: 460
  sheet: -2.07 (0.55), residues: 68
  loop : -2.29 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 268 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.027   0.002   PHE G  67 
 TYR   0.026   0.001   TYR F  80 
 ARG   0.005   0.000   ARG B 150 

*********************** 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
  312 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5944 (tpp) cc_final: 0.5357 (ptt)
REVERT: F   78 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7655 (tptt)
REVERT: F  278 MET cc_start: 0.8936 (ttp) cc_final: 0.8723 (ttp)
REVERT: G   20 MET cc_start: 0.6917 (tmm) cc_final: 0.6507 (tmm)
REVERT: G   28 SER cc_start: 0.8852 (m) cc_final: 0.8252 (t)
REVERT: G  100 MET cc_start: 0.7725 (tpp) cc_final: 0.7366 (tpp)
REVERT: G  108 LYS cc_start: 0.7609 (tmtt) cc_final: 0.6894 (tttt)
REVERT: G  118 MET cc_start: 0.8013 (tpp) cc_final: 0.7644 (mmt)
REVERT: G  120 ILE cc_start: 0.8872 (pt) cc_final: 0.8669 (mm)
REVERT: G  270 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8128 (mtp180)
REVERT: G  356 LEU cc_start: 0.7737 (pp) cc_final: 0.7277 (pp)
REVERT: A    9 LEU cc_start: 0.9400 (mt) cc_final: 0.8618 (mt)
REVERT: A   42 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8292 (mtmm)
REVERT: A   48 MET cc_start: 0.8061 (ttm) cc_final: 0.7338 (ttm)
REVERT: A  103 LEU cc_start: 0.8879 (mt) cc_final: 0.8667 (mt)
REVERT: A  107 ASP cc_start: 0.7898 (p0) cc_final: 0.7108 (m-30)
REVERT: A  128 GLU cc_start: 0.7379 (pm20) cc_final: 0.7145 (pm20)
REVERT: B    8 ASN cc_start: 0.8023 (m110) cc_final: 0.6942 (m-40)
REVERT: B   20 GLU cc_start: 0.6348 (pp20) cc_final: 0.5944 (pp20)
REVERT: B   64 ASP cc_start: 0.8037 (m-30) cc_final: 0.7776 (m-30)
REVERT: B   82 TYR cc_start: 0.8709 (t80) cc_final: 0.8220 (t80)
REVERT: B  100 MET cc_start: 0.7409 (mmm) cc_final: 0.7009 (mmm)
REVERT: B  126 HIS cc_start: 0.8240 (m-70) cc_final: 0.7674 (m170)
REVERT: B  145 ARG cc_start: 0.9139 (mtm-85) cc_final: 0.8612 (mtm180)
REVERT: B  186 SER cc_start: 0.9133 (m) cc_final: 0.8755 (p)
REVERT: C    6 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6165 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 312
  average time/residue: 0.1792
  time to fit residues: 75.9911
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  : 0.880 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0030
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN

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 = 0.141620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.117787 restraints weight = 12495.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.120337 restraints weight = 8244.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.122029 restraints weight = 6176.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7406  Z= 0.159
  Angle     :  0.697  11.545  10023  Z= 0.337
  Chirality :  0.044   0.234   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.623  86.480   1050
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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: -2.47 (0.27), residues: 911
  helix: -1.17 (0.25), residues: 461
  sheet: -2.01 (0.61), residues: 58
  loop : -2.06 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C   7 
 HIS   0.002   0.000   HIS A  73 
 PHE   0.027   0.001   PHE G  67 
 TYR   0.017   0.001   TYR A  96 
 ARG   0.003   0.000   ARG G 133 

*********************** 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
  292 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5902 (tpp) cc_final: 0.5177 (ptt)
REVERT: F   67 SER cc_start: 0.9529 (p) cc_final: 0.9292 (t)
REVERT: G   20 MET cc_start: 0.6840 (tmm) cc_final: 0.6422 (tmm)
REVERT: G   28 SER cc_start: 0.8820 (m) cc_final: 0.8218 (t)
REVERT: G   62 LYS cc_start: 0.9208 (tptt) cc_final: 0.8509 (tppt)
REVERT: G  100 MET cc_start: 0.7604 (tpp) cc_final: 0.7056 (tpp)
REVERT: G  108 LYS cc_start: 0.7723 (tmtt) cc_final: 0.7010 (tttt)
REVERT: G  115 LEU cc_start: 0.8729 (mt) cc_final: 0.8427 (pp)
REVERT: G  270 ARG cc_start: 0.8266 (mtp180) cc_final: 0.8027 (mtp180)
REVERT: A    9 LEU cc_start: 0.9333 (mt) cc_final: 0.8449 (mt)
REVERT: A   42 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8270 (mtmm)
REVERT: A   48 MET cc_start: 0.8121 (ttm) cc_final: 0.7340 (ttm)
REVERT: A  103 LEU cc_start: 0.8919 (mt) cc_final: 0.8717 (mt)
REVERT: A  107 ASP cc_start: 0.7841 (p0) cc_final: 0.7124 (m-30)
REVERT: A  108 ASP cc_start: 0.8763 (p0) cc_final: 0.8402 (p0)
REVERT: B   38 ASN cc_start: 0.8471 (p0) cc_final: 0.8175 (p0)
REVERT: B   82 TYR cc_start: 0.8726 (t80) cc_final: 0.8215 (t80)
REVERT: B  100 MET cc_start: 0.7298 (mmm) cc_final: 0.6946 (mmm)
REVERT: B  126 HIS cc_start: 0.8130 (m-70) cc_final: 0.7544 (m170)
REVERT: B  145 ARG cc_start: 0.9106 (mtm-85) cc_final: 0.8649 (mtm180)
REVERT: B  186 SER cc_start: 0.9097 (m) cc_final: 0.8683 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.1823
  time to fit residues: 71.6543
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  : 0.783 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0010
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   8 ASN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.140663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.116734 restraints weight = 12316.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.119204 restraints weight = 8212.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.120916 restraints weight = 6207.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5070

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= 0.202
  Angle     :  0.726  11.871  10023  Z= 0.353
  Chirality :  0.045   0.235   1205
  Planarity :  0.005   0.045   1246
  Dihedral  :  7.691  82.706   1050
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.43 (0.27), residues: 911
  helix: -1.13 (0.24), residues: 475
  sheet: -1.94 (0.57), residues: 68
  loop : -2.06 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 330 
 HIS   0.004   0.001   HIS F  89 
 PHE   0.059   0.002   PHE G  67 
 TYR   0.012   0.001   TYR F   6 
 ARG   0.003   0.000   ARG G 133 

*********************** 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
  289 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.6053 (tpp) cc_final: 0.5399 (ptt)
REVERT: F  297 LEU cc_start: 0.9363 (tp) cc_final: 0.9107 (tp)
REVERT: G   20 MET cc_start: 0.6989 (tmm) cc_final: 0.6562 (tmm)
REVERT: G   28 SER cc_start: 0.8850 (m) cc_final: 0.8222 (t)
REVERT: G  100 MET cc_start: 0.7744 (tpp) cc_final: 0.7237 (tpp)
REVERT: G  108 LYS cc_start: 0.7761 (tmtt) cc_final: 0.7050 (tttt)
REVERT: G  270 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8057 (mtp180)
REVERT: G  356 LEU cc_start: 0.7958 (pp) cc_final: 0.7732 (pp)
REVERT: G  357 MET cc_start: 0.7821 (mmt) cc_final: 0.7579 (mmt)
REVERT: A    7 LYS cc_start: 0.8127 (tptp) cc_final: 0.7777 (mtmt)
REVERT: A    9 LEU cc_start: 0.9372 (mt) cc_final: 0.9062 (mp)
REVERT: A   42 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8364 (mtmm)
REVERT: A   48 MET cc_start: 0.8236 (ttm) cc_final: 0.7988 (ttm)
REVERT: A  107 ASP cc_start: 0.7884 (p0) cc_final: 0.7194 (m-30)
REVERT: A  108 ASP cc_start: 0.8722 (p0) cc_final: 0.8435 (p0)
REVERT: A  194 ASP cc_start: 0.7690 (t0) cc_final: 0.7462 (t0)
REVERT: B    8 ASN cc_start: 0.8006 (m110) cc_final: 0.6869 (m110)
REVERT: B   38 ASN cc_start: 0.8590 (p0) cc_final: 0.8260 (p0)
REVERT: B   67 ILE cc_start: 0.9080 (pt) cc_final: 0.8869 (pt)
REVERT: B   82 TYR cc_start: 0.8763 (t80) cc_final: 0.8256 (t80)
REVERT: B  100 MET cc_start: 0.7190 (mmm) cc_final: 0.6791 (mmm)
REVERT: B  120 GLU cc_start: 0.8089 (pm20) cc_final: 0.7888 (pm20)
REVERT: B  126 HIS cc_start: 0.8203 (m-70) cc_final: 0.7615 (m170)
REVERT: B  145 ARG cc_start: 0.9121 (mtm-85) cc_final: 0.8684 (mtm180)
REVERT: B  186 SER cc_start: 0.9183 (m) cc_final: 0.8740 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1785
  time to fit residues: 69.6600
Evaluate side-chains
  246 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3597 r_free = 0.3597 target = 0.143177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.118940 restraints weight = 12335.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.121592 restraints weight = 8014.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.123370 restraints weight = 5940.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.5237

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= 0.172
  Angle     :  0.736  14.658  10023  Z= 0.348
  Chirality :  0.044   0.245   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.576  80.426   1050
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.20 (0.28), residues: 911
  helix: -0.94 (0.25), residues: 470
  sheet: -1.73 (0.65), residues: 58
  loop : -1.97 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 268 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.052   0.002   PHE G  67 
 TYR   0.019   0.001   TYR B  96 
 ARG   0.003   0.000   ARG G 133 

*********************** 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
  297 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5900 (tpp) cc_final: 0.5211 (ptt)
REVERT: F   72 LEU cc_start: 0.9368 (tp) cc_final: 0.9005 (tt)
REVERT: F  105 LEU cc_start: 0.9128 (pp) cc_final: 0.8924 (pp)
REVERT: F  297 LEU cc_start: 0.9290 (tp) cc_final: 0.9049 (tp)
REVERT: G   20 MET cc_start: 0.7021 (tmm) cc_final: 0.6630 (tmm)
REVERT: G   28 SER cc_start: 0.8834 (m) cc_final: 0.8189 (t)
REVERT: G  100 MET cc_start: 0.7498 (tpp) cc_final: 0.6940 (tpp)
REVERT: G  108 LYS cc_start: 0.7817 (tmtt) cc_final: 0.7147 (tttt)
REVERT: G  270 ARG cc_start: 0.8242 (mtp180) cc_final: 0.7996 (mtp180)
REVERT: G  357 MET cc_start: 0.7853 (mmt) cc_final: 0.7612 (mmt)
REVERT: A    7 LYS cc_start: 0.8082 (tptp) cc_final: 0.7735 (mtmt)
REVERT: A    9 LEU cc_start: 0.9329 (mt) cc_final: 0.9015 (mp)
REVERT: A   42 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8326 (mtmm)
REVERT: A   48 MET cc_start: 0.8189 (ttm) cc_final: 0.7949 (ttm)
REVERT: A  107 ASP cc_start: 0.7797 (p0) cc_final: 0.7132 (m-30)
REVERT: A  108 ASP cc_start: 0.8715 (p0) cc_final: 0.8448 (p0)
REVERT: A  194 ASP cc_start: 0.7626 (t0) cc_final: 0.7402 (t0)
REVERT: A  218 HIS cc_start: 0.8837 (p-80) cc_final: 0.8630 (p-80)
REVERT: B   38 ASN cc_start: 0.8571 (p0) cc_final: 0.8301 (p0)
REVERT: B   82 TYR cc_start: 0.8691 (t80) cc_final: 0.8163 (t80)
REVERT: B  100 MET cc_start: 0.7081 (mmm) cc_final: 0.6686 (mmm)
REVERT: B  126 HIS cc_start: 0.8148 (m-70) cc_final: 0.7524 (m170)
REVERT: B  145 ARG cc_start: 0.9112 (mtm-85) cc_final: 0.8673 (mtm180)
REVERT: B  186 SER cc_start: 0.9185 (m) cc_final: 0.8819 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.1758
  time to fit residues: 70.4002
Evaluate side-chains
  246 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 50 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 80 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 4 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 128 GLN
A 104 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.115292 restraints weight = 12604.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117864 restraints weight = 8300.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.119592 restraints weight = 6224.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.5327

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= 0.178
  Angle     :  0.724  12.632  10023  Z= 0.345
  Chirality :  0.044   0.234   1205
  Planarity :  0.005   0.046   1246
  Dihedral  :  7.524  78.666   1050
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.06 (0.28), residues: 911
  helix: -0.79 (0.25), residues: 471
  sheet: -1.58 (0.65), residues: 58
  loop : -1.98 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 330 
 HIS   0.003   0.001   HIS F  89 
 PHE   0.050   0.002   PHE G  67 
 TYR   0.009   0.001   TYR F  80 
 ARG   0.003   0.000   ARG G 133 

*********************** 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  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   59 MET cc_start: 0.5723 (tpp) cc_final: 0.5085 (ptt)
REVERT: F   72 LEU cc_start: 0.9336 (tp) cc_final: 0.8905 (tt)
REVERT: F  297 LEU cc_start: 0.9350 (tp) cc_final: 0.9115 (tp)
REVERT: G   20 MET cc_start: 0.6936 (tmm) cc_final: 0.6530 (tmm)
REVERT: G   28 SER cc_start: 0.8733 (m) cc_final: 0.8239 (t)
REVERT: G  100 MET cc_start: 0.7644 (tpp) cc_final: 0.7067 (tpp)
REVERT: G  108 LYS cc_start: 0.7731 (tmtt) cc_final: 0.7092 (tttt)
REVERT: G  357 MET cc_start: 0.7870 (mmt) cc_final: 0.7607 (mmt)
REVERT: A    7 LYS cc_start: 0.8163 (tptp) cc_final: 0.7787 (mtmt)
REVERT: A    9 LEU cc_start: 0.9353 (mt) cc_final: 0.9046 (mp)
REVERT: A   42 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8407 (mtmm)
REVERT: A   48 MET cc_start: 0.8310 (ttm) cc_final: 0.8050 (ttm)
REVERT: A  107 ASP cc_start: 0.7974 (p0) cc_final: 0.7232 (m-30)
REVERT: A  108 ASP cc_start: 0.8748 (p0) cc_final: 0.8469 (p0)
REVERT: A  116 ASP cc_start: 0.7827 (t0) cc_final: 0.6728 (t0)
REVERT: A  194 ASP cc_start: 0.7749 (t0) cc_final: 0.7497 (t0)
REVERT: A  218 HIS cc_start: 0.8861 (p-80) cc_final: 0.8609 (p-80)
REVERT: B    8 ASN cc_start: 0.8141 (m110) cc_final: 0.7169 (m110)
REVERT: B   38 ASN cc_start: 0.8763 (p0) cc_final: 0.8462 (p0)
REVERT: B   82 TYR cc_start: 0.8697 (t80) cc_final: 0.8221 (t80)
REVERT: B  100 MET cc_start: 0.7392 (mmm) cc_final: 0.7038 (mmm)
REVERT: B  122 MET cc_start: 0.8704 (mtm) cc_final: 0.8130 (mtm)
REVERT: B  126 HIS cc_start: 0.8311 (m-70) cc_final: 0.8044 (m170)
REVERT: B  186 SER cc_start: 0.9265 (m) cc_final: 0.8768 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1767
  time to fit residues: 69.1445
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  : 0.804 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0370
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0030
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.1672

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  65 GLN
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.138725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.113995 restraints weight = 12730.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.116515 restraints weight = 8405.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118261 restraints weight = 6338.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.5446

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= 0.196
  Angle     :  0.749  11.303  10023  Z= 0.361
  Chirality :  0.045   0.236   1205
  Planarity :  0.005   0.047   1246
  Dihedral  :  7.537  77.223   1050
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.28), residues: 911
  helix: -0.71 (0.25), residues: 474
  sheet: -1.62 (0.67), residues: 58
  loop : -1.95 (0.32), residues: 379

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   0.047   0.002   PHE G  67 
 TYR   0.022   0.001   TYR B  96 
 ARG   0.003   0.000   ARG G 133 

********************** 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
  284 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   26 PHE cc_start: 0.7821 (m-10) cc_final: 0.7478 (m-10)
REVERT: F   59 MET cc_start: 0.5750 (tpp) cc_final: 0.5227 (ptt)
REVERT: F   72 LEU cc_start: 0.9386 (tp) cc_final: 0.8990 (tt)
REVERT: F   82 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7187 (tm-30)
REVERT: F  282 MET cc_start: 0.8560 (tmm) cc_final: 0.8360 (tmm)
REVERT: F  297 LEU cc_start: 0.9314 (tp) cc_final: 0.9073 (tp)
REVERT: G   20 MET cc_start: 0.6911 (tmm) cc_final: 0.6568 (tmm)
REVERT: G   28 SER cc_start: 0.8804 (m) cc_final: 0.8174 (t)
REVERT: G  100 MET cc_start: 0.7569 (tpp) cc_final: 0.7071 (tpp)
REVERT: G  108 LYS cc_start: 0.7894 (tmtt) cc_final: 0.7156 (tttt)
REVERT: A    7 LYS cc_start: 0.8110 (tptp) cc_final: 0.7776 (mtmt)
REVERT: A    9 LEU cc_start: 0.9352 (mt) cc_final: 0.8926 (mp)
REVERT: A   42 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8417 (mtmm)
REVERT: A   48 MET cc_start: 0.8257 (ttm) cc_final: 0.7901 (ttm)
REVERT: A  107 ASP cc_start: 0.7819 (p0) cc_final: 0.7208 (m-30)
REVERT: A  108 ASP cc_start: 0.8637 (p0) cc_final: 0.8396 (p0)
REVERT: A  194 ASP cc_start: 0.7681 (t0) cc_final: 0.7385 (t0)
REVERT: A  218 HIS cc_start: 0.8826 (p-80) cc_final: 0.8623 (p-80)
REVERT: B    8 ASN cc_start: 0.8068 (m110) cc_final: 0.7474 (m110)
REVERT: B   30 GLU cc_start: 0.8353 (pm20) cc_final: 0.8115 (pm20)
REVERT: B   38 ASN cc_start: 0.8683 (p0) cc_final: 0.8458 (p0)
REVERT: B   82 TYR cc_start: 0.8675 (t80) cc_final: 0.8163 (t80)
REVERT: B  100 MET cc_start: 0.7191 (mmm) cc_final: 0.6829 (mmm)
REVERT: B  126 HIS cc_start: 0.8101 (m-70) cc_final: 0.7738 (m170)
REVERT: B  186 SER cc_start: 0.9268 (m) cc_final: 0.8908 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.1810
  time to fit residues: 70.4924
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  : 0.930 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 13 optimal weight:    0.0040
   chunk 10 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  98 ASN
** B  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.141054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116183 restraints weight = 12412.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.118863 restraints weight = 8026.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120622 restraints weight = 5970.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.5582

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= 0.169
  Angle     :  0.736  11.035  10023  Z= 0.350
  Chirality :  0.044   0.230   1205
  Planarity :  0.004   0.046   1246
  Dihedral  :  7.394  76.021   1050
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.51 %
    Favored  : 99.36 %
  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: -1.74 (0.28), residues: 911
  helix: -0.49 (0.25), residues: 458
  sheet: -1.50 (0.68), residues: 58
  loop : -1.84 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F 330 
 HIS   0.003   0.000   HIS F  89 
 PHE   0.042   0.001   PHE G  67 
 TYR   0.016   0.001   TYR A  96 
 ARG   0.003   0.000   ARG G 133 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2537.30 seconds
wall clock time: 46 minutes 16.78 seconds (2776.78 seconds total)