Starting phenix.real_space_refine
on Fri Aug 22 22:10:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xqr_38586/08_2025/8xqr_38586.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5274      2.51       5
     N    1432      2.21       5
     O    1516      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8273
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1964
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2616
          Classifications: {'peptide': 341}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 981
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 981
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "R"
      Number of atoms: 2256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2256
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 3, 'TRANS': 275}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'FLF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.68, per 1000 atoms: 0.20
  Number of scatterers: 8273
  At special positions: 0
  Unit cell: (74.88, 99.84, 131.04, 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      48     16.00
     F       3      9.00
     O    1516      8.00
     N    1432      7.00
     C    5274      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 100 " - pdb=" SG  CYS N 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 416.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      45.6% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 35
    Processing helix  chain 'A' and resid 48 through 60
      removed outlier: 3.920A  pdb=" N   ILE A  58 " --> pdb=" O   LYS A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
      removed outlier: 3.634A  pdb=" N   ASN A 104 " --> pdb=" O   GLN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 134
    Processing helix  chain 'A' and resid 148 through 159
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.216A  pdb=" N   TYR A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.777A  pdb=" N   ALA A 171 " --> pdb=" O   PRO A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 206
      removed outlier: 3.537A  pdb=" N   THR A 190 " --> pdb=" O   ASP A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 247
      removed outlier: 3.943A  pdb=" N   ASN A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.640A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 33
      removed outlier: 3.608A  pdb=" N   ASN N  32 " --> pdb=" O   THR N  29 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR N  33 " --> pdb=" O   PHE N  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 29 through 33'
    Processing helix  chain 'N' and resid 63 through 66
    Processing helix  chain 'N' and resid 88 through 92
    Processing helix  chain 'R' and resid 3 through 37
    Processing helix  chain 'R' and resid 42 through 72
    Processing helix  chain 'R' and resid 74 through 78
    Processing helix  chain 'R' and resid 80 through 112
    Processing helix  chain 'R' and resid 116 through 124
      removed outlier: 3.568A  pdb=" N   TRP R 124 " --> pdb=" O   LEU R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 125 through 158
      removed outlier: 4.096A  pdb=" N   VAL R 139 " --> pdb=" O   LEU R 135 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE R 140 " --> pdb=" O   VAL R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 215
      Proline residue:  R 190  - end of helix
    Processing helix  chain 'R' and resid 225 through 254
    Processing helix  chain 'R' and resid 258 through 284
      removed outlier: 3.647A  pdb=" N   ILE R 263 " --> pdb=" O   GLU R 259 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   TYR R 272 " --> pdb=" O   MET R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
      removed outlier: 3.811A  pdb=" N   SER R 277 " --> pdb=" O   PRO R 273 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 299
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 79
      removed outlier: 9.316A  pdb=" N   ALA A 108 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ARG A  38 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   ILE A 110 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU A  40 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   VAL A 112 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE A 109 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   PHE A 111 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52
      removed outlier: 6.206A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.700A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.572A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.141A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.626A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.747A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.687A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
    Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 61
      removed outlier: 6.620A  pdb=" N   TRP N  37 " --> pdb=" O   VAL N  49 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1335 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: 1.34

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2677
        1.34 -     1.46: 1752
        1.46 -     1.58: 3943
        1.58 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 8441
  Sorted by residual:
  bond pdb=" N   FLF R 501 "
       pdb=" C1' FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.414 -0.037 2.00e-02 2.50e+03 3.42e+00
  bond pdb=" CA  ASN A 119 "
       pdb=" CB  ASN A 119 "
    ideal  model  delta    sigma   weight residual
    1.536  1.566 -0.031 2.01e-02 2.48e+03 2.33e+00
  bond pdb=" N   FLF R 501 "
       pdb=" C6  FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.378  1.407 -0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" C1  FLF R 501 "
       pdb=" C7  FLF R 501 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 2.00e-02 2.50e+03 1.60e+00
  bond pdb=" CB  ASN A 104 "
       pdb=" CG  ASN A 104 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.14e+00
  ... (remaining 8436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 11342
        2.99 -     5.99: 66
        5.99 -     8.98: 7
        8.98 -    11.97: 1
       11.97 -    14.97: 1
  Bond angle restraints: 11417
  Sorted by residual:
  angle pdb=" CA  LEU R 257 "
        pdb=" CB  LEU R 257 "
        pdb=" CG  LEU R 257 "
      ideal   model   delta    sigma   weight residual
     116.30  131.27  -14.97 3.50e+00 8.16e-02 1.83e+01
  angle pdb=" CB  LEU R 257 "
        pdb=" CG  LEU R 257 "
        pdb=" CD1 LEU R 257 "
      ideal   model   delta    sigma   weight residual
     110.70  119.47   -8.77 3.00e+00 1.11e-01 8.55e+00
  angle pdb=" CB  MET B 262 "
        pdb=" CG  MET B 262 "
        pdb=" SD  MET B 262 "
      ideal   model   delta    sigma   weight residual
     112.70  103.95    8.75 3.00e+00 1.11e-01 8.51e+00
  angle pdb=" CA  LYS R 210 "
        pdb=" CB  LYS R 210 "
        pdb=" CG  LYS R 210 "
      ideal   model   delta    sigma   weight residual
     114.10  119.75   -5.65 2.00e+00 2.50e-01 7.98e+00
  angle pdb=" CA  LEU B  55 "
        pdb=" CB  LEU B  55 "
        pdb=" CG  LEU B  55 "
      ideal   model   delta    sigma   weight residual
     116.30  125.45   -9.15 3.50e+00 8.16e-02 6.83e+00
  ... (remaining 11412 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 4306
       16.94 -    33.88: 534
       33.88 -    50.81: 132
       50.81 -    67.75: 21
       67.75 -    84.69: 3
  Dihedral angle restraints: 4996
    sinusoidal: 1971
      harmonic: 3025
  Sorted by residual:
  dihedral pdb=" CB  CYS N 100 "
           pdb=" SG  CYS N 100 "
           pdb=" SG  CYS N 108 "
           pdb=" CB  CYS N 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.57   45.57     1      1.00e+01 1.00e-02 2.88e+01
  dihedral pdb=" CG  ARG B  96 "
           pdb=" CD  ARG B  96 "
           pdb=" NE  ARG B  96 "
           pdb=" CZ  ARG B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   38.08   51.92     2      1.50e+01 4.44e-03 1.32e+01
  dihedral pdb=" SG  CYS N 100 "
           pdb=" CB  CYS N 108 "
           pdb=" SG  CYS N 108 "
           pdb=" CA  CYS N 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   20.80   58.20     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 4993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1047
       0.050 -    0.101: 188
       0.101 -    0.151: 52
       0.151 -    0.202: 3
       0.202 -    0.252: 3
  Chirality restraints: 1293
  Sorted by residual:
  chirality pdb=" CG  LEU R 131 "
            pdb=" CB  LEU R 131 "
            pdb=" CD1 LEU R 131 "
            pdb=" CD2 LEU R 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  LYS R 210 "
            pdb=" N   LYS R 210 "
            pdb=" C   LYS R 210 "
            pdb=" CB  LYS R 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CG  LEU R 257 "
            pdb=" CB  LEU R 257 "
            pdb=" CD1 LEU R 257 "
            pdb=" CD2 LEU R 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1290 not shown)

  Planarity restraints: 1439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R  72 "   -0.058 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO R  73 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO R  73 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R  73 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 340 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.74e+00
        pdb=" CG  ASN B 340 "   -0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 340 "    0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 340 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  54 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.58e+00
        pdb=" N   PRO C  55 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1436 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 174
        2.66 -     3.22: 8170
        3.22 -     3.78: 13781
        3.78 -     4.34: 17914
        4.34 -     4.90: 29470
  Nonbonded interactions: 69509
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  93 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.104 3.120
  nonbonded pdb=" O   GLY B 162 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OD1 ASP B 153 "
            pdb=" N   ASP B 154 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" O   PRO A 187 "
            pdb=" OG1 THR A 190 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" O   ILE B 273 "
     model   vdw
     2.194 3.120
  ... (remaining 69504 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
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      :  0.004   0.039   8443  Z= 0.190
  Angle     :  0.635  14.966  11421  Z= 0.334
  Chirality :  0.043   0.252   1293
  Planarity :  0.005   0.089   1439
  Dihedral  : 15.580  84.687   3030
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 30.04 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.27), residues: 1030
  helix:  2.28 (0.24), residues: 428
  sheet: -0.14 (0.36), residues: 221
  loop : -0.60 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  96 
 TYR   0.011   0.001   TYR R 272 
 PHE   0.027   0.002   PHE R 119 
 TRP   0.027   0.002   TRP R  66 
 HIS   0.011   0.002   HIS R 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8441)
  covalent geometry    : angle       0.63560 (11417)
  SS BOND              : bond        0.00111 (    2)
  SS BOND              : angle       0.12815 (    4)
  hydrogen bonds       : bond        0.17781 (  464)
  hydrogen bonds       : angle       6.57062 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7453 (ptp-110)
REVERT: A  148 LYS cc_start: 0.8748 (mptt) cc_final: 0.8450 (mttt)
REVERT: B  219 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7783 (ttm-80)
REVERT: N   50 SER cc_start: 0.8688 (m) cc_final: 0.8393 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1046
  time to fit residues: 36.2635
Evaluate side-chains
  263 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0470
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1682

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 134 ASN
B 155 ASN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.146477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.125732 restraints weight = 12956.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.52
r_work: 0.3461 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.0953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8443  Z= 0.246
  Angle     :  0.617  10.248  11421  Z= 0.328
  Chirality :  0.043   0.148   1293
  Planarity :  0.005   0.053   1439
  Dihedral  :  4.508  39.018   1129
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.11 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.17 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.27), residues: 1030
  helix:  2.46 (0.24), residues: 428
  sheet: -0.11 (0.35), residues: 229
  loop : -0.79 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  96 
 TYR   0.016   0.002   TYR R 272 
 PHE   0.015   0.002   PHE R  17 
 TRP   0.014   0.002   TRP A  99 
 HIS   0.008   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 8441)
  covalent geometry    : angle       0.61742 (11417)
  SS BOND              : bond        0.00164 (    2)
  SS BOND              : angle       0.47973 (    4)
  hydrogen bonds       : bond        0.04872 (  464)
  hydrogen bonds       : angle       4.94361 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 282
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7803 (mtpt)
REVERT: B  155 ASN cc_start: 0.8223 (t0) cc_final: 0.7927 (t0)
REVERT: B  271 CYS cc_start: 0.8407 (p) cc_final: 0.8169 (p)
REVERT: B  291 ASP cc_start: 0.7190 (p0) cc_final: 0.6881 (p0)
REVERT: B  303 ASP cc_start: 0.7147 (m-30) cc_final: 0.6841 (m-30)
REVERT: N   50 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8300 (p)
REVERT: N  113 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7666 (p)
REVERT: R    6 LYS cc_start: 0.7936 (tppt) cc_final: 0.7393 (tppt)
REVERT: R   62 ILE cc_start: 0.8238 (mm) cc_final: 0.7786 (tp)
REVERT: R  131 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8469 (mm)
REVERT: R  212 MET cc_start: 0.7722 (mmm) cc_final: 0.7456 (mmp)
REVERT: R  268 MET cc_start: 0.8087 (tmm) cc_final: 0.7858 (tmm)
REVERT: R  285 LYS cc_start: 0.8004 (tttt) cc_final: 0.7672 (tttt)
  outliers start: 44
  outliers final: 27
  residues processed: 302
  average time/residue: 0.1069
  time to fit residues: 41.6938
Evaluate side-chains
  306 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 275
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   50 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  113 SER
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  207 LYS
Chi-restraints excluded: chain R residue  294 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 90 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A  31 GLN
A 134 ASN
B 220 GLN
B 259 GLN
R 284 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.146959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.126157 restraints weight = 12821.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.53
r_work: 0.3487 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8443  Z= 0.164
  Angle     :  0.546   9.230  11421  Z= 0.289
  Chirality :  0.041   0.154   1293
  Planarity :  0.004   0.048   1439
  Dihedral  :  4.254  27.490   1129
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.62 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 23.61 %
    Favored  : 70.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.27), residues: 1030
  helix:  2.47 (0.24), residues: 434
  sheet: -0.02 (0.34), residues: 221
  loop : -0.84 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  96 
 TYR   0.012   0.002   TYR B 264 
 PHE   0.012   0.001   PHE B 253 
 TRP   0.014   0.002   TRP A  99 
 HIS   0.008   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8441)
  covalent geometry    : angle       0.54627 (11417)
  SS BOND              : bond        0.00179 (    2)
  SS BOND              : angle       0.39474 (    4)
  hydrogen bonds       : bond        0.04308 (  464)
  hydrogen bonds       : angle       4.65853 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 275
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7734 (mtpt)
REVERT: A  104 ASN cc_start: 0.8577 (p0) cc_final: 0.8175 (p0)
REVERT: A  120 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7564 (mtt-85)
REVERT: A  236 ASP cc_start: 0.8558 (t0) cc_final: 0.8317 (t0)
REVERT: A  238 ILE cc_start: 0.8146 (mm) cc_final: 0.7905 (mt)
REVERT: B   68 ARG cc_start: 0.7718 (mtt-85) cc_final: 0.7312 (mtt-85)
REVERT: B  153 ASP cc_start: 0.7917 (t0) cc_final: 0.7701 (t0)
REVERT: B  155 ASN cc_start: 0.8154 (t0) cc_final: 0.7804 (t0)
REVERT: B  262 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7336 (mtt)
REVERT: B  271 CYS cc_start: 0.8481 (p) cc_final: 0.8239 (p)
REVERT: B  291 ASP cc_start: 0.7157 (p0) cc_final: 0.6773 (p0)
REVERT: B  303 ASP cc_start: 0.7115 (m-30) cc_final: 0.6809 (m-30)
REVERT: N   50 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8237 (p)
REVERT: N  113 SER cc_start: 0.7972 (m) cc_final: 0.7681 (p)
REVERT: R   62 ILE cc_start: 0.8163 (mm) cc_final: 0.7737 (tp)
REVERT: R  131 LEU cc_start: 0.8713 (mm) cc_final: 0.8464 (mm)
REVERT: R  205 MET cc_start: 0.7962 (mmm) cc_final: 0.7738 (tpp)
REVERT: R  210 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7769 (mmtt)
REVERT: R  212 MET cc_start: 0.7734 (mmm) cc_final: 0.7422 (mmp)
REVERT: R  268 MET cc_start: 0.8069 (tmm) cc_final: 0.7738 (tmm)
REVERT: R  285 LYS cc_start: 0.7931 (tttt) cc_final: 0.7586 (tttt)
  outliers start: 50
  outliers final: 33
  residues processed: 301
  average time/residue: 0.0978
  time to fit residues: 38.3606
Evaluate side-chains
  306 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 270
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   47 GLU
Chi-restraints excluded: chain N residue   50 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   22 LEU
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  207 LYS
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 134 ASN
B 220 GLN
** N  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.145911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.125258 restraints weight = 13065.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.55
r_work: 0.3466 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8443  Z= 0.185
  Angle     :  0.550   9.929  11421  Z= 0.289
  Chirality :  0.041   0.154   1293
  Planarity :  0.004   0.045   1439
  Dihedral  :  4.173  23.595   1129
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.82 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 23.39 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.26), residues: 1030
  helix:  2.45 (0.24), residues: 436
  sheet: -0.00 (0.34), residues: 220
  loop : -0.91 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  96 
 TYR   0.012   0.002   TYR N  96 
 PHE   0.017   0.002   PHE R 119 
 TRP   0.015   0.002   TRP A  99 
 HIS   0.008   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8441)
  covalent geometry    : angle       0.54969 (11417)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.19037 (    4)
  hydrogen bonds       : bond        0.04209 (  464)
  hydrogen bonds       : angle       4.55868 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 278
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7493 (tmmm)
REVERT: A  120 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7538 (mtt-85)
REVERT: A  236 ASP cc_start: 0.8573 (t0) cc_final: 0.8232 (t0)
REVERT: B  118 ASP cc_start: 0.7910 (p0) cc_final: 0.7540 (p0)
REVERT: B  153 ASP cc_start: 0.7950 (t0) cc_final: 0.7643 (t0)
REVERT: B  155 ASN cc_start: 0.8111 (t0) cc_final: 0.7752 (t0)
REVERT: B  262 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7322 (mtt)
REVERT: B  291 ASP cc_start: 0.7197 (p0) cc_final: 0.6887 (p0)
REVERT: B  303 ASP cc_start: 0.7112 (m-30) cc_final: 0.6791 (m-30)
REVERT: N   50 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (p)
REVERT: N  113 SER cc_start: 0.8102 (m) cc_final: 0.7799 (p)
REVERT: R   62 ILE cc_start: 0.8178 (mm) cc_final: 0.7745 (tp)
REVERT: R  131 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: R  132 VAL cc_start: 0.7985 (p) cc_final: 0.7714 (m)
REVERT: R  210 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7709 (mmtt)
REVERT: R  212 MET cc_start: 0.7771 (mmm) cc_final: 0.7470 (mmp)
REVERT: R  268 MET cc_start: 0.8080 (tmm) cc_final: 0.7641 (tmm)
REVERT: R  284 ASN cc_start: 0.8318 (t0) cc_final: 0.8042 (t0)
  outliers start: 54
  outliers final: 37
  residues processed: 306
  average time/residue: 0.0967
  time to fit residues: 38.8610
Evaluate side-chains
  314 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 273
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue   47 GLU
Chi-restraints excluded: chain N residue   50 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  207 LYS
Chi-restraints excluded: chain R residue  294 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    0.0970
   chunk 59 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 67 optimal weight:    0.4980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A  31 GLN
A 134 ASN
B 220 GLN
B 295 ASN
** N  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  31 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.148726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.128669 restraints weight = 12963.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.50
r_work: 0.3485 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8443  Z= 0.154
  Angle     :  0.538  10.036  11421  Z= 0.282
  Chirality :  0.040   0.156   1293
  Planarity :  0.004   0.050   1439
  Dihedral  :  4.084  21.584   1129
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.72 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 24.17 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1030
  helix:  2.50 (0.24), residues: 436
  sheet: -0.10 (0.34), residues: 222
  loop : -0.86 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  96 
 TYR   0.011   0.001   TYR N  96 
 PHE   0.019   0.001   PHE R 119 
 TRP   0.014   0.001   TRP A  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8441)
  covalent geometry    : angle       0.53826 (11417)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       0.23988 (    4)
  hydrogen bonds       : bond        0.03974 (  464)
  hydrogen bonds       : angle       4.45700 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 275
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7473 (tmmm)
REVERT: A   54 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7710 (mtpt)
REVERT: A  120 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7569 (mtt-85)
REVERT: A  236 ASP cc_start: 0.8544 (t0) cc_final: 0.8279 (t0)
REVERT: A  238 ILE cc_start: 0.8150 (mm) cc_final: 0.7918 (mt)
REVERT: B  118 ASP cc_start: 0.7914 (p0) cc_final: 0.7543 (p0)
REVERT: B  153 ASP cc_start: 0.7928 (t0) cc_final: 0.7531 (t0)
REVERT: B  155 ASN cc_start: 0.8087 (t0) cc_final: 0.7709 (t0)
REVERT: B  186 ASP cc_start: 0.7693 (m-30) cc_final: 0.7288 (m-30)
REVERT: B  262 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7252 (mtt)
REVERT: B  269 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8401 (pt)
REVERT: B  291 ASP cc_start: 0.7212 (p0) cc_final: 0.6828 (p0)
REVERT: B  303 ASP cc_start: 0.7118 (m-30) cc_final: 0.6794 (m-30)
REVERT: B  337 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8283 (mtpp)
REVERT: N   50 SER cc_start: 0.8434 (m) cc_final: 0.8229 (p)
REVERT: N  113 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7761 (p)
REVERT: R   62 ILE cc_start: 0.8162 (mm) cc_final: 0.7757 (tp)
REVERT: R  119 PHE cc_start: 0.8122 (t80) cc_final: 0.7806 (t80)
REVERT: R  131 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8480 (mm)
REVERT: R  132 VAL cc_start: 0.7962 (p) cc_final: 0.7684 (m)
REVERT: R  205 MET cc_start: 0.7978 (mmm) cc_final: 0.7766 (tpp)
REVERT: R  210 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7736 (mmtt)
REVERT: R  212 MET cc_start: 0.7740 (mmm) cc_final: 0.7459 (mmp)
REVERT: R  248 PHE cc_start: 0.7830 (t80) cc_final: 0.7581 (t80)
REVERT: R  268 MET cc_start: 0.8106 (tmm) cc_final: 0.7626 (tmm)
REVERT: R  282 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8035 (tt)
  outliers start: 57
  outliers final: 39
  residues processed: 304
  average time/residue: 0.1042
  time to fit residues: 41.3786
Evaluate side-chains
  319 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 273
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  113 SER
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  207 LYS
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0870
   chunk 80 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.148813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128639 restraints weight = 12867.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.50
r_work: 0.3493 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8443  Z= 0.155
  Angle     :  0.536   7.276  11421  Z= 0.281
  Chirality :  0.040   0.163   1293
  Planarity :  0.004   0.046   1439
  Dihedral  :  4.054  19.208   1129
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.72 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 23.50 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1030
  helix:  2.52 (0.24), residues: 436
  sheet: -0.11 (0.33), residues: 225
  loop : -0.85 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  96 
 TYR   0.012   0.001   TYR N  96 
 PHE   0.013   0.001   PHE R 119 
 TRP   0.013   0.001   TRP A  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8441)
  covalent geometry    : angle       0.53571 (11417)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.23633 (    4)
  hydrogen bonds       : bond        0.03916 (  464)
  hydrogen bonds       : angle       4.43208 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 277
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7480 (tmmm)
REVERT: A   54 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7735 (mtpt)
REVERT: A  104 ASN cc_start: 0.8549 (p0) cc_final: 0.8197 (p0)
REVERT: A  120 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7558 (mtt-85)
REVERT: A  177 GLU cc_start: 0.7066 (pm20) cc_final: 0.6833 (pm20)
REVERT: A  236 ASP cc_start: 0.8549 (t0) cc_final: 0.8186 (t0)
REVERT: A  238 ILE cc_start: 0.8178 (mm) cc_final: 0.7926 (mt)
REVERT: A  240 LYS cc_start: 0.8383 (mttm) cc_final: 0.8151 (mttm)
REVERT: B   68 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7379 (mtt-85)
REVERT: B   96 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7431 (mtp85)
REVERT: B  118 ASP cc_start: 0.7903 (p0) cc_final: 0.7542 (p0)
REVERT: B  153 ASP cc_start: 0.7945 (t0) cc_final: 0.7569 (t0)
REVERT: B  155 ASN cc_start: 0.8100 (t0) cc_final: 0.7698 (t0)
REVERT: B  186 ASP cc_start: 0.7665 (m-30) cc_final: 0.7305 (m-30)
REVERT: B  218 CYS cc_start: 0.8268 (p) cc_final: 0.8059 (p)
REVERT: B  262 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7249 (mtt)
REVERT: B  269 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8395 (pt)
REVERT: B  291 ASP cc_start: 0.7223 (p0) cc_final: 0.6814 (p0)
REVERT: B  303 ASP cc_start: 0.7133 (m-30) cc_final: 0.6797 (m-30)
REVERT: B  337 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8397 (mtpp)
REVERT: N  113 SER cc_start: 0.8028 (m) cc_final: 0.7751 (p)
REVERT: R   31 ASN cc_start: 0.8283 (m-40) cc_final: 0.7901 (m-40)
REVERT: R   62 ILE cc_start: 0.8213 (mm) cc_final: 0.7812 (tp)
REVERT: R  119 PHE cc_start: 0.8229 (t80) cc_final: 0.7879 (t80)
REVERT: R  131 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8451 (mm)
REVERT: R  210 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7782 (mmtt)
REVERT: R  212 MET cc_start: 0.7709 (mmm) cc_final: 0.7504 (mmp)
REVERT: R  248 PHE cc_start: 0.7868 (t80) cc_final: 0.7607 (t80)
REVERT: R  268 MET cc_start: 0.8143 (tmm) cc_final: 0.7650 (tmm)
REVERT: R  282 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8065 (tt)
  outliers start: 59
  outliers final: 45
  residues processed: 309
  average time/residue: 0.0956
  time to fit residues: 38.7386
Evaluate side-chains
  323 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 272
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.148231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128149 restraints weight = 13001.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.55
r_work: 0.3482 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8443  Z= 0.176
  Angle     :  0.553   9.855  11421  Z= 0.291
  Chirality :  0.041   0.161   1293
  Planarity :  0.004   0.045   1439
  Dihedral  :  4.106  18.914   1129
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 24.72 %
    Favored  : 68.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1030
  helix:  2.51 (0.24), residues: 435
  sheet:  0.02 (0.34), residues: 208
  loop : -0.93 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 197 
 TYR   0.013   0.001   TYR N  96 
 PHE   0.013   0.001   PHE R 236 
 TRP   0.013   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8441)
  covalent geometry    : angle       0.55262 (11417)
  SS BOND              : bond        0.00118 (    2)
  SS BOND              : angle       0.19047 (    4)
  hydrogen bonds       : bond        0.03997 (  464)
  hydrogen bonds       : angle       4.45178 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 273
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7514 (tmmm)
REVERT: A   54 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7715 (mtpt)
REVERT: A   95 GLU cc_start: 0.7222 (mm-30) cc_final: 0.7002 (mm-30)
REVERT: A  104 ASN cc_start: 0.8525 (p0) cc_final: 0.8111 (p0)
REVERT: A  120 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7645 (mtt-85)
REVERT: A  177 GLU cc_start: 0.7099 (pm20) cc_final: 0.6836 (pm20)
REVERT: A  236 ASP cc_start: 0.8554 (t0) cc_final: 0.8264 (t0)
REVERT: B   49 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7665 (mtm-85)
REVERT: B   68 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7505 (mtt-85)
REVERT: B   96 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7303 (mtp85)
REVERT: B  118 ASP cc_start: 0.7912 (p0) cc_final: 0.7556 (p0)
REVERT: B  153 ASP cc_start: 0.7998 (t0) cc_final: 0.7628 (t0)
REVERT: B  155 ASN cc_start: 0.8097 (t0) cc_final: 0.7693 (t0)
REVERT: B  186 ASP cc_start: 0.7724 (m-30) cc_final: 0.7365 (m-30)
REVERT: B  218 CYS cc_start: 0.8222 (p) cc_final: 0.7975 (p)
REVERT: B  262 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7322 (mtt)
REVERT: B  269 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (pt)
REVERT: B  291 ASP cc_start: 0.7234 (p0) cc_final: 0.6826 (p0)
REVERT: B  303 ASP cc_start: 0.7148 (m-30) cc_final: 0.6805 (m-30)
REVERT: B  337 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8384 (mtpp)
REVERT: N  113 SER cc_start: 0.8000 (m) cc_final: 0.7730 (p)
REVERT: R   31 ASN cc_start: 0.8312 (m-40) cc_final: 0.7922 (m-40)
REVERT: R   62 ILE cc_start: 0.8175 (mm) cc_final: 0.7771 (tp)
REVERT: R  111 ILE cc_start: 0.8739 (mt) cc_final: 0.8495 (mt)
REVERT: R  210 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7767 (mmtt)
REVERT: R  212 MET cc_start: 0.7662 (mmm) cc_final: 0.7380 (mmp)
REVERT: R  248 PHE cc_start: 0.7919 (t80) cc_final: 0.7657 (t80)
REVERT: R  268 MET cc_start: 0.8142 (tmm) cc_final: 0.7623 (tmm)
REVERT: R  282 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (tt)
  outliers start: 59
  outliers final: 45
  residues processed: 304
  average time/residue: 0.0959
  time to fit residues: 38.2401
Evaluate side-chains
  320 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 270
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  244 LYS
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  111 VAL
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 54 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0570
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.148969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.128882 restraints weight = 12879.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.53
r_work: 0.3500 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8443  Z= 0.150
  Angle     :  0.549   9.633  11421  Z= 0.288
  Chirality :  0.041   0.188   1293
  Planarity :  0.004   0.047   1439
  Dihedral  :  4.062  18.224   1129
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 25.94 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.26), residues: 1030
  helix:  2.53 (0.24), residues: 435
  sheet:  0.07 (0.34), residues: 208
  loop : -0.92 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 197 
 TYR   0.012   0.001   TYR N  96 
 PHE   0.025   0.001   PHE R 119 
 TRP   0.014   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8441)
  covalent geometry    : angle       0.54930 (11417)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.23362 (    4)
  hydrogen bonds       : bond        0.03892 (  464)
  hydrogen bonds       : angle       4.42947 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 271
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7514 (tmmm)
REVERT: A  104 ASN cc_start: 0.8462 (p0) cc_final: 0.8056 (p0)
REVERT: A  120 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7547 (mtt-85)
REVERT: A  177 GLU cc_start: 0.7013 (pm20) cc_final: 0.6749 (pm20)
REVERT: A  236 ASP cc_start: 0.8568 (t0) cc_final: 0.8154 (t0)
REVERT: A  238 ILE cc_start: 0.8139 (mm) cc_final: 0.7913 (mt)
REVERT: A  240 LYS cc_start: 0.8443 (mttp) cc_final: 0.8234 (mttm)
REVERT: B   49 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7636 (mtm-85)
REVERT: B   96 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7383 (mtp85)
REVERT: B  118 ASP cc_start: 0.7891 (p0) cc_final: 0.7537 (p0)
REVERT: B  137 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7793 (mmm-85)
REVERT: B  153 ASP cc_start: 0.7973 (t0) cc_final: 0.7615 (t0)
REVERT: B  155 ASN cc_start: 0.8082 (t0) cc_final: 0.7677 (t0)
REVERT: B  186 ASP cc_start: 0.7688 (m-30) cc_final: 0.7328 (m-30)
REVERT: B  218 CYS cc_start: 0.8208 (p) cc_final: 0.7964 (p)
REVERT: B  262 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7248 (mtt)
REVERT: B  269 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8389 (pt)
REVERT: B  291 ASP cc_start: 0.7225 (p0) cc_final: 0.6792 (p0)
REVERT: B  303 ASP cc_start: 0.7108 (m-30) cc_final: 0.6767 (m-30)
REVERT: B  337 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8365 (mtpp)
REVERT: N   60 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7900 (p)
REVERT: N  113 SER cc_start: 0.7959 (m) cc_final: 0.7707 (p)
REVERT: R   31 ASN cc_start: 0.8337 (m-40) cc_final: 0.7955 (m-40)
REVERT: R   62 ILE cc_start: 0.8163 (mm) cc_final: 0.7815 (tp)
REVERT: R  111 ILE cc_start: 0.8725 (mt) cc_final: 0.8500 (mt)
REVERT: R  210 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7785 (mmtt)
REVERT: R  212 MET cc_start: 0.7677 (mmm) cc_final: 0.7378 (mmp)
REVERT: R  248 PHE cc_start: 0.7876 (t80) cc_final: 0.7616 (t80)
REVERT: R  268 MET cc_start: 0.8089 (tmm) cc_final: 0.7539 (tmm)
REVERT: R  270 MET cc_start: 0.8177 (mmm) cc_final: 0.7839 (mmm)
REVERT: R  282 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8079 (tt)
  outliers start: 50
  outliers final: 42
  residues processed: 302
  average time/residue: 0.0963
  time to fit residues: 38.0758
Evaluate side-chains
  313 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 266
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    0.3980
   chunk 38 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  19 ASN
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.148782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128684 restraints weight = 12976.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.54
r_work: 0.3483 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8443  Z= 0.155
  Angle     :  0.553   8.192  11421  Z= 0.291
  Chirality :  0.041   0.160   1293
  Planarity :  0.004   0.046   1439
  Dihedral  :  4.047  18.352   1129
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 25.50 %
    Favored  : 68.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.26), residues: 1030
  helix:  2.51 (0.24), residues: 435
  sheet:  0.06 (0.34), residues: 208
  loop : -0.88 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 197 
 TYR   0.012   0.001   TYR N  96 
 PHE   0.012   0.001   PHE R 236 
 TRP   0.013   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8441)
  covalent geometry    : angle       0.55353 (11417)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.28244 (    4)
  hydrogen bonds       : bond        0.03890 (  464)
  hydrogen bonds       : angle       4.40183 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 273
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7191 (mmtm)
REVERT: A   21 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7535 (tmmm)
REVERT: A   75 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8015 (t)
REVERT: A  104 ASN cc_start: 0.8490 (p0) cc_final: 0.8132 (p0)
REVERT: A  120 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7497 (mtt-85)
REVERT: A  177 GLU cc_start: 0.7011 (pm20) cc_final: 0.6721 (pm20)
REVERT: A  236 ASP cc_start: 0.8567 (t0) cc_final: 0.8182 (t0)
REVERT: B   49 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7618 (mtm-85)
REVERT: B   96 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7375 (mtp85)
REVERT: B  118 ASP cc_start: 0.7905 (p0) cc_final: 0.7557 (p0)
REVERT: B  137 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7718 (mtp-110)
REVERT: B  153 ASP cc_start: 0.7972 (t0) cc_final: 0.7628 (t0)
REVERT: B  155 ASN cc_start: 0.8085 (t0) cc_final: 0.7662 (t0)
REVERT: B  186 ASP cc_start: 0.7708 (m-30) cc_final: 0.7375 (m-30)
REVERT: B  218 CYS cc_start: 0.8232 (p) cc_final: 0.7991 (p)
REVERT: B  262 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7295 (mtt)
REVERT: B  269 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (pt)
REVERT: B  291 ASP cc_start: 0.7236 (p0) cc_final: 0.6776 (p0)
REVERT: B  303 ASP cc_start: 0.7121 (m-30) cc_final: 0.6770 (m-30)
REVERT: B  337 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8400 (mtpp)
REVERT: N   60 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7890 (p)
REVERT: R   31 ASN cc_start: 0.8306 (m-40) cc_final: 0.7944 (m-40)
REVERT: R   62 ILE cc_start: 0.8169 (mm) cc_final: 0.7823 (tp)
REVERT: R  111 ILE cc_start: 0.8704 (mt) cc_final: 0.8478 (mt)
REVERT: R  119 PHE cc_start: 0.8197 (t80) cc_final: 0.7836 (t80)
REVERT: R  210 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7781 (mmtt)
REVERT: R  212 MET cc_start: 0.7733 (mmm) cc_final: 0.7431 (mmp)
REVERT: R  248 PHE cc_start: 0.7850 (t80) cc_final: 0.7599 (t80)
REVERT: R  268 MET cc_start: 0.8099 (tmm) cc_final: 0.7559 (tmm)
REVERT: R  270 MET cc_start: 0.8238 (mmm) cc_final: 0.7866 (mmm)
REVERT: R  282 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8100 (tt)
REVERT: R  287 LEU cc_start: 0.8227 (mt) cc_final: 0.8017 (mp)
  outliers start: 53
  outliers final: 43
  residues processed: 301
  average time/residue: 0.0946
  time to fit residues: 37.5829
Evaluate side-chains
  316 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 267
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.145935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.125571 restraints weight = 12845.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.54
r_work: 0.3467 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8443  Z= 0.176
  Angle     :  0.571   9.479  11421  Z= 0.301
  Chirality :  0.042   0.223   1293
  Planarity :  0.004   0.057   1439
  Dihedral  :  4.111  19.275   1129
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.30 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 26.16 %
    Favored  : 68.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.26), residues: 1030
  helix:  2.45 (0.24), residues: 435
  sheet: -0.03 (0.34), residues: 210
  loop : -0.92 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  96 
 TYR   0.014   0.001   TYR N  96 
 PHE   0.013   0.001   PHE R 236 
 TRP   0.012   0.001   TRP A  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8441)
  covalent geometry    : angle       0.57136 (11417)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.21650 (    4)
  hydrogen bonds       : bond        0.03994 (  464)
  hydrogen bonds       : angle       4.43994 ( 1335)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 271
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7182 (mmtm)
REVERT: A   21 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7480 (tmmm)
REVERT: A   54 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7709 (mtpt)
REVERT: A   75 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8025 (t)
REVERT: A  104 ASN cc_start: 0.8490 (p0) cc_final: 0.8117 (p0)
REVERT: A  120 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7528 (mtt-85)
REVERT: A  177 GLU cc_start: 0.7097 (pm20) cc_final: 0.6806 (pm20)
REVERT: A  199 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6719 (mm-30)
REVERT: A  236 ASP cc_start: 0.8583 (t0) cc_final: 0.8268 (t0)
REVERT: B   49 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7635 (mtm-85)
REVERT: B   68 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7485 (mtt-85)
REVERT: B   96 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7382 (mtp85)
REVERT: B  118 ASP cc_start: 0.7901 (p0) cc_final: 0.7562 (p0)
REVERT: B  137 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7773 (mtp-110)
REVERT: B  153 ASP cc_start: 0.8000 (t0) cc_final: 0.7677 (t0)
REVERT: B  155 ASN cc_start: 0.8097 (t0) cc_final: 0.7674 (t0)
REVERT: B  186 ASP cc_start: 0.7772 (m-30) cc_final: 0.7389 (m-30)
REVERT: B  218 CYS cc_start: 0.8243 (p) cc_final: 0.7994 (p)
REVERT: B  262 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (mtt)
REVERT: B  269 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8410 (pt)
REVERT: B  291 ASP cc_start: 0.7243 (p0) cc_final: 0.6788 (p0)
REVERT: B  303 ASP cc_start: 0.7091 (m-30) cc_final: 0.6748 (m-30)
REVERT: B  337 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8290 (mtpp)
REVERT: N   60 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7895 (p)
REVERT: R   31 ASN cc_start: 0.8292 (m-40) cc_final: 0.7935 (m-40)
REVERT: R   62 ILE cc_start: 0.8174 (mm) cc_final: 0.7953 (mm)
REVERT: R  210 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7763 (mmtt)
REVERT: R  212 MET cc_start: 0.7786 (mmm) cc_final: 0.7502 (mmp)
REVERT: R  248 PHE cc_start: 0.7900 (t80) cc_final: 0.7647 (t80)
REVERT: R  268 MET cc_start: 0.8088 (tmm) cc_final: 0.7527 (tmm)
  outliers start: 51
  outliers final: 43
  residues processed: 299
  average time/residue: 0.0901
  time to fit residues: 35.4777
Evaluate side-chains
  319 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 270
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LYS
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   54 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain N residue    8 SER
Chi-restraints excluded: chain N residue   60 SER
Chi-restraints excluded: chain N residue   62 THR
Chi-restraints excluded: chain N residue   70 THR
Chi-restraints excluded: chain N residue   79 THR
Chi-restraints excluded: chain N residue  100 CYS
Chi-restraints excluded: chain N residue  109 PHE
Chi-restraints excluded: chain N residue  115 THR
Chi-restraints excluded: chain N residue  127 VAL
Chi-restraints excluded: chain R residue    4 VAL
Chi-restraints excluded: chain R residue   49 THR
Chi-restraints excluded: chain R residue  118 ILE
Chi-restraints excluded: chain R residue  122 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  140 PHE
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  257 LEU
Chi-restraints excluded: chain R residue  294 VAL
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
A 134 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.146156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.125794 restraints weight = 12978.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.52
r_work: 0.3475 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8443  Z= 0.163
  Angle     :  0.580  10.975  11421  Z= 0.302
  Chirality :  0.042   0.215   1293
  Planarity :  0.004   0.063   1439
  Dihedral  :  4.099  18.806   1129
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.01 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 26.61 %
    Favored  : 67.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.26), residues: 1030
  helix:  2.44 (0.24), residues: 435
  sheet:  0.03 (0.34), residues: 210
  loop : -0.90 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 197 
 TYR   0.012   0.001   TYR N  96 
 PHE   0.011   0.001   PHE R  26 
 TRP   0.014   0.001   TRP B  99 
 HIS   0.009   0.001   HIS R  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8441)
  covalent geometry    : angle       0.58022 (11417)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.23197 (    4)
  hydrogen bonds       : bond        0.03948 (  464)
  hydrogen bonds       : angle       4.44019 ( 1335)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1760.17 seconds
wall clock time: 30 minutes 52.99 seconds (1852.99 seconds total)