Starting phenix.real_space_refine
on Sat Dec 28 07:41:34 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hj0_33482/12_2024/8hj0_33482.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5250      2.51       5
     N    1427      2.21       5
     O    1531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8260
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1966
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      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: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2297
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
  Time building chain proxies: 4.93, per 1000 atoms: 0.60
  Number of scatterers: 8260
  At special positions: 0
  Unit cell: (88.4, 102.96, 127.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1531      8.00
     N    1427      7.00
     C    5250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 122 " - pdb=" SG  CYS R 149 " distance=2.05

  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      42.5% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 4.105A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 3.905A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 3.821A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 322 through 342
      removed outlier: 3.836A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 382
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.986A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 4.887A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.507A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.755A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 26 through 56
      removed outlier: 4.382A  pdb=" N   ILE R  34 " --> pdb=" O   LEU R  30 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE R  35 " --> pdb=" O   GLU R  31 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER R  44 " --> pdb=" O   VAL R  40 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY R  45 " --> pdb=" O   LEU R  41 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ASN R  46 " --> pdb=" O   ILE R  42 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE R  48 " --> pdb=" O   SER R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 61
    Processing helix  chain 'R' and resid 62 through 80
      removed outlier: 4.079A  pdb=" N   TYR R  66 " --> pdb=" O   HIS R  62 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE R  67 " --> pdb=" O   THR R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 91
      removed outlier: 4.174A  pdb=" N   SER R  86 " --> pdb=" O   CYS R  82 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   HIS R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 133
      removed outlier: 4.286A  pdb=" N   ILE R 104 " --> pdb=" O   LEU R 100 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL R 111 " --> pdb=" O   PHE R 107 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER R 114 " --> pdb=" O   SER R 110 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 141
    Processing helix  chain 'R' and resid 142 through 161
      removed outlier: 3.683A  pdb=" N   PHE R 161 " --> pdb=" O   SER R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 162 through 165
    Processing helix  chain 'R' and resid 188 through 197
    Processing helix  chain 'R' and resid 199 through 231
      removed outlier: 4.139A  pdb=" N   ALA R 203 " --> pdb=" O   LEU R 199 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA R 204 " --> pdb=" O   TYR R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 278
      Proline residue:  R 267  - end of helix
    Processing helix  chain 'R' and resid 282 through 295
    Processing helix  chain 'R' and resid 298 through 308
      removed outlier: 3.747A  pdb=" N   VAL R 302 " --> pdb=" O   PHE R 298 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE R 303 " --> pdb=" O   CYS R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 322
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.791A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.581A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.517A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 4.402A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 4.066A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.791A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.435A  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: 4.004A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.030A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 4.136A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1179 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: 2.57

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2702
        1.35 -     1.48: 2214
        1.48 -     1.62: 3457
        1.62 -     1.75: 0
        1.75 -     1.88: 70
  Bond restraints: 8443
  Sorted by residual:
  bond pdb=" CB  CYS R 149 "
       pdb=" SG  CYS R 149 "
    ideal  model  delta    sigma   weight residual
    1.808  1.877 -0.069 3.30e-02 9.18e+02 4.38e+00
  bond pdb=" CA  ALA B 328 "
       pdb=" CB  ALA B 328 "
    ideal  model  delta    sigma   weight residual
    1.526  1.494  0.032 1.70e-02 3.46e+03 3.61e+00
  bond pdb=" C   VAL R  84 "
       pdb=" N   PRO R  85 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.024 1.28e-02 6.10e+03 3.46e+00
  bond pdb=" C   ASN R 300 "
       pdb=" N   PRO R 301 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.025 1.36e-02 5.41e+03 3.43e+00
  bond pdb=" CB  ASP R 126 "
       pdb=" CG  ASP R 126 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.38e+00
  ... (remaining 8438 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 10889
        2.21 -     4.41: 474
        4.41 -     6.62: 59
        6.62 -     8.82: 18
        8.82 -    11.03: 9
  Bond angle restraints: 11449
  Sorted by residual:
  angle pdb=" C   ASP B 195 "
        pdb=" N   THR B 196 "
        pdb=" CA  THR B 196 "
      ideal   model   delta    sigma   weight residual
     121.54  131.27   -9.73 1.91e+00 2.74e-01 2.60e+01
  angle pdb=" C   GLU R  97 "
        pdb=" N   GLU R  98 "
        pdb=" CA  GLU R  98 "
      ideal   model   delta    sigma   weight residual
     121.54  130.46   -8.92 1.91e+00 2.74e-01 2.18e+01
  angle pdb=" CA  ASP R 126 "
        pdb=" CB  ASP R 126 "
        pdb=" CG  ASP R 126 "
      ideal   model   delta    sigma   weight residual
     112.60  116.75   -4.15 1.00e+00 1.00e+00 1.72e+01
  angle pdb=" CB  ARG R 256 "
        pdb=" CG  ARG R 256 "
        pdb=" CD  ARG R 256 "
      ideal   model   delta    sigma   weight residual
     111.30  119.61   -8.31 2.30e+00 1.89e-01 1.30e+01
  angle pdb=" N   CYS N  96 "
        pdb=" CA  CYS N  96 "
        pdb=" C   CYS N  96 "
      ideal   model   delta    sigma   weight residual
     110.48  105.27    5.21 1.48e+00 4.57e-01 1.24e+01
  ... (remaining 11444 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4488
       17.97 -    35.94: 410
       35.94 -    53.91: 80
       53.91 -    71.88: 13
       71.88 -    89.84: 11
  Dihedral angle restraints: 5002
    sinusoidal: 1963
      harmonic: 3039
  Sorted by residual:
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.33   78.67     1      1.00e+01 1.00e-02 7.71e+01
  dihedral pdb=" CB  CYS R 122 "
           pdb=" SG  CYS R 122 "
           pdb=" SG  CYS R 149 "
           pdb=" CB  CYS R 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.02  -66.02     1      1.00e+01 1.00e-02 5.70e+01
  dihedral pdb=" CA  SER R 307 "
           pdb=" C   SER R 307 "
           pdb=" N   ASP R 308 "
           pdb=" CA  ASP R 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.42  -23.58     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 4999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1091
       0.078 -    0.155: 171
       0.155 -    0.232: 21
       0.232 -    0.310: 1
       0.310 -    0.387: 3
  Chirality restraints: 1287
  Sorted by residual:
  chirality pdb=" CB  THR B  47 "
            pdb=" CA  THR B  47 "
            pdb=" OG1 THR B  47 "
            pdb=" CG2 THR B  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.16    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" CB  ILE N  51 "
            pdb=" CA  ILE N  51 "
            pdb=" CG1 ILE N  51 "
            pdb=" CG2 ILE N  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" CB  ILE B 269 "
            pdb=" CA  ILE B 269 "
            pdb=" CG1 ILE B 269 "
            pdb=" CG2 ILE B 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.73e+00
  ... (remaining 1284 not shown)

  Planarity restraints: 1457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN N  13 "   -0.077 5.00e-02 4.00e+02   1.17e-01 2.18e+01
        pdb=" N   PRO N  14 "    0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO N  14 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO N  14 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 215 "   -0.024 2.00e-02 2.50e+03   2.69e-02 1.26e+01
        pdb=" CG  PHE R 215 "    0.063 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 215 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 215 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 215 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 215 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 215 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 124 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   SER R 124 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER R 124 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ILE R 125 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1454 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1882
        2.78 -     3.31: 7840
        3.31 -     3.84: 14430
        3.84 -     4.37: 17211
        4.37 -     4.90: 28894
  Nonbonded interactions: 70257
  Sorted by model distance:
  nonbonded pdb=" O   VAL R  83 "
            pdb=" OG  SER R  86 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER B 275 "
            pdb=" O   SER B 316 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   CYS B 204 "
            pdb=" OH  TYR N 117 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   TRP R 180 "
            pdb=" OG  SER R 184 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.266 3.040
  ... (remaining 70252 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:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.300
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8443  Z= 0.364
  Angle     :  1.070  11.028  11449  Z= 0.598
  Chirality :  0.058   0.387   1287
  Planarity :  0.008   0.117   1457
  Dihedral  : 14.888  89.844   3024
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.24), residues: 1029
  helix: -0.90 (0.24), residues: 401
  sheet: -0.79 (0.33), residues: 214
  loop : -1.73 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP R 180 
 HIS   0.015   0.002   HIS A 220 
 PHE   0.063   0.004   PHE R 215 
 TYR   0.021   0.003   TYR A 348 
 ARG   0.026   0.002   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: B  111 TYR cc_start: 0.6383 (m-80) cc_final: 0.6142 (m-80)
REVERT: G   21 MET cc_start: 0.4214 (mmm) cc_final: 0.2584 (mtm)
REVERT: R   31 GLU cc_start: 0.5584 (mm-30) cc_final: 0.4817 (mm-30)
REVERT: R  152 LEU cc_start: 0.6932 (mt) cc_final: 0.6605 (mp)
REVERT: R  287 PHE cc_start: 0.5795 (t80) cc_final: 0.5311 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2479
  time to fit residues: 64.9084
Evaluate side-chains
  154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 79 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
B  35 ASN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8443  Z= 0.192
  Angle     :  0.588   5.754  11449  Z= 0.316
  Chirality :  0.043   0.140   1287
  Planarity :  0.005   0.083   1457
  Dihedral  :  5.275  22.001   1136
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.97 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1029
  helix:  0.31 (0.25), residues: 410
  sheet: -0.73 (0.33), residues: 223
  loop : -1.50 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.018   0.002   PHE R 272 
 TYR   0.010   0.001   TYR B 264 
 ARG   0.007   0.000   ARG N  67 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 180
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A   60 MET cc_start: 0.6833 (mpp) cc_final: 0.6529 (mpp)
REVERT: A  325 THR cc_start: 0.8116 (m) cc_final: 0.7886 (m)
REVERT: B  118 ASP cc_start: 0.5918 (t70) cc_final: 0.5464 (t0)
REVERT: B  325 MET cc_start: 0.7011 (mmt) cc_final: 0.6427 (mmt)
REVERT: G   21 MET cc_start: 0.4118 (mmm) cc_final: 0.2525 (mtt)
REVERT: R  152 LEU cc_start: 0.7024 (mt) cc_final: 0.6533 (mp)
REVERT: R  194 PHE cc_start: 0.6339 (m-80) cc_final: 0.6039 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 186
  average time/residue: 0.2558
  time to fit residues: 61.6041
Evaluate side-chains
  163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue  123 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 361 ASN
B  17 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  69 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8443  Z= 0.299
  Angle     :  0.635   6.344  11449  Z= 0.342
  Chirality :  0.046   0.186   1287
  Planarity :  0.005   0.073   1457
  Dihedral  :  5.323  21.941   1136
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 12.96 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.25), residues: 1029
  helix:  0.46 (0.25), residues: 410
  sheet: -0.83 (0.32), residues: 221
  loop : -1.36 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.008   0.002   HIS B  91 
 PHE   0.013   0.002   PHE B 151 
 TYR   0.015   0.002   TYR B 264 
 ARG   0.008   0.001   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 164
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   60 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6524 (mpp)
REVERT: A  256 LEU cc_start: 0.8121 (mt) cc_final: 0.7903 (mt)
REVERT: A  325 THR cc_start: 0.8200 (m) cc_final: 0.7938 (m)
REVERT: B   43 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7482 (mp)
REVERT: B  118 ASP cc_start: 0.6248 (t70) cc_final: 0.5751 (t70)
REVERT: B  247 ASP cc_start: 0.7349 (p0) cc_final: 0.6910 (p0)
REVERT: R  152 LEU cc_start: 0.7167 (mt) cc_final: 0.6614 (mp)
  outliers start: 29
  outliers final: 21
  residues processed: 184
  average time/residue: 0.2345
  time to fit residues: 57.3721
Evaluate side-chains
  175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain R residue   84 VAL
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 87 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 361 ASN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6501
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      :  0.003   0.051   8443  Z= 0.198
  Angle     :  0.570   6.612  11449  Z= 0.304
  Chirality :  0.043   0.236   1287
  Planarity :  0.004   0.069   1457
  Dihedral  :  4.943  21.799   1136
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.95 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.26), residues: 1029
  helix:  0.85 (0.25), residues: 409
  sheet: -0.72 (0.33), residues: 221
  loop : -1.30 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 271 
 HIS   0.007   0.001   HIS B  91 
 PHE   0.018   0.002   PHE R 194 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.006   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6481 (mpp)
REVERT: A  325 THR cc_start: 0.8126 (m) cc_final: 0.7864 (m)
REVERT: B  118 ASP cc_start: 0.6148 (t70) cc_final: 0.5713 (t70)
REVERT: B  275 SER cc_start: 0.8113 (t) cc_final: 0.7453 (m)
REVERT: N  120 GLN cc_start: 0.5758 (mm-40) cc_final: 0.5491 (mm-40)
  outliers start: 27
  outliers final: 21
  residues processed: 181
  average time/residue: 0.2432
  time to fit residues: 57.9233
Evaluate side-chains
  183 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   98 GLU
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 87 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
R  46 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.078   8443  Z= 0.493
  Angle     :  0.763   7.023  11449  Z= 0.410
  Chirality :  0.053   0.249   1287
  Planarity :  0.007   0.098   1457
  Dihedral  :  5.715  22.101   1136
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 16.39 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1029
  helix:  0.40 (0.25), residues: 408
  sheet: -0.76 (0.33), residues: 213
  loop : -1.57 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 271 
 HIS   0.008   0.002   HIS A 347 
 PHE   0.021   0.003   PHE R 194 
 TYR   0.017   0.003   TYR B 264 
 ARG   0.009   0.001   ARG A 270 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 159
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A  325 THR cc_start: 0.8418 (m) cc_final: 0.8088 (m)
REVERT: B   43 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7674 (mp)
REVERT: B  118 ASP cc_start: 0.6329 (t70) cc_final: 0.5823 (t70)
REVERT: B  247 ASP cc_start: 0.7430 (p0) cc_final: 0.7028 (p0)
REVERT: N  115 TYR cc_start: 0.7614 (t80) cc_final: 0.7260 (t80)
REVERT: N  120 GLN cc_start: 0.6108 (mm-40) cc_final: 0.5663 (mm-40)
  outliers start: 43
  outliers final: 33
  residues processed: 189
  average time/residue: 0.2405
  time to fit residues: 60.3993
Evaluate side-chains
  191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  254 ASN
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   68 PHE
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8443  Z= 0.209
  Angle     :  0.588   8.188  11449  Z= 0.313
  Chirality :  0.044   0.232   1287
  Planarity :  0.004   0.061   1457
  Dihedral  :  5.008  21.944   1136
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.16 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.25), residues: 1029
  helix:  0.85 (0.25), residues: 408
  sheet: -0.69 (0.33), residues: 218
  loop : -1.46 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 271 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.019   0.002   PHE R 272 
 TYR   0.015   0.002   TYR N  95 
 ARG   0.007   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 170
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  325 THR cc_start: 0.8264 (m) cc_final: 0.7950 (m)
REVERT: B   43 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7434 (mp)
REVERT: B  118 ASP cc_start: 0.6123 (t70) cc_final: 0.5702 (t70)
REVERT: B  247 ASP cc_start: 0.7377 (p0) cc_final: 0.6919 (p0)
REVERT: B  325 MET cc_start: 0.7160 (mmt) cc_final: 0.6959 (mmt)
REVERT: N   72 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6727 (ptm160)
REVERT: N  120 GLN cc_start: 0.5869 (mm-40) cc_final: 0.5489 (mm-40)
  outliers start: 35
  outliers final: 29
  residues processed: 192
  average time/residue: 0.2532
  time to fit residues: 63.5077
Evaluate side-chains
  198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0980
   chunk 82 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6466
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8443  Z= 0.164
  Angle     :  0.552   6.331  11449  Z= 0.293
  Chirality :  0.043   0.200   1287
  Planarity :  0.004   0.056   1457
  Dihedral  :  4.585  21.607   1136
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.71 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.26), residues: 1029
  helix:  1.31 (0.26), residues: 409
  sheet: -0.41 (0.35), residues: 206
  loop : -1.41 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.024   0.002   PHE R 194 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.007   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 172
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLN cc_start: 0.5838 (mt0) cc_final: 0.5497 (mp10)
REVERT: A  239 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7292 (t0)
REVERT: A  325 THR cc_start: 0.8073 (m) cc_final: 0.7826 (m)
REVERT: B  118 ASP cc_start: 0.5866 (t70) cc_final: 0.5484 (t0)
REVERT: B  200 VAL cc_start: 0.8445 (p) cc_final: 0.8204 (t)
REVERT: B  234 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6866 (m-80)
REVERT: B  247 ASP cc_start: 0.7351 (p0) cc_final: 0.6955 (p0)
REVERT: B  275 SER cc_start: 0.7905 (t) cc_final: 0.7338 (m)
REVERT: N  120 GLN cc_start: 0.5667 (mm-40) cc_final: 0.5460 (mm-40)
REVERT: R   31 GLU cc_start: 0.6018 (mm-30) cc_final: 0.5279 (mm-30)
REVERT: R  287 PHE cc_start: 0.6080 (t80) cc_final: 0.5749 (t80)
  outliers start: 35
  outliers final: 26
  residues processed: 196
  average time/residue: 0.2428
  time to fit residues: 62.6902
Evaluate side-chains
  194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   chunk 48 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8443  Z= 0.183
  Angle     :  0.573  14.143  11449  Z= 0.299
  Chirality :  0.043   0.206   1287
  Planarity :  0.004   0.055   1457
  Dihedral  :  4.567  21.296   1136
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.04 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.26), residues: 1029
  helix:  1.40 (0.26), residues: 409
  sheet: -0.40 (0.34), residues: 211
  loop : -1.36 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 271 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.035   0.002   PHE R 194 
 TYR   0.014   0.001   TYR N 117 
 ARG   0.007   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLN cc_start: 0.5899 (mt0) cc_final: 0.5556 (mp10)
REVERT: A  239 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7630 (t0)
REVERT: A  325 THR cc_start: 0.8092 (m) cc_final: 0.7848 (m)
REVERT: A  346 ARG cc_start: 0.6844 (mpp80) cc_final: 0.5803 (mtp85)
REVERT: B   43 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7445 (mp)
REVERT: B  118 ASP cc_start: 0.5976 (t70) cc_final: 0.5564 (t70)
REVERT: B  200 VAL cc_start: 0.8481 (p) cc_final: 0.8233 (t)
REVERT: B  247 ASP cc_start: 0.7359 (p0) cc_final: 0.6917 (p0)
REVERT: B  275 SER cc_start: 0.7980 (t) cc_final: 0.7390 (m)
REVERT: N  120 GLN cc_start: 0.5684 (mm-40) cc_final: 0.5477 (mm-40)
  outliers start: 36
  outliers final: 29
  residues processed: 188
  average time/residue: 0.2458
  time to fit residues: 60.7475
Evaluate side-chains
  191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8443  Z= 0.185
  Angle     :  0.581  14.076  11449  Z= 0.302
  Chirality :  0.044   0.187   1287
  Planarity :  0.004   0.059   1457
  Dihedral  :  4.549  20.904   1136
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.27 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1029
  helix:  1.38 (0.25), residues: 409
  sheet: -0.40 (0.35), residues: 212
  loop : -1.32 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 271 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.031   0.002   PHE R 194 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.006   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 160
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7640 (t0)
REVERT: A  325 THR cc_start: 0.8098 (m) cc_final: 0.7857 (m)
REVERT: A  346 ARG cc_start: 0.6981 (mpp80) cc_final: 0.5901 (mtp85)
REVERT: B   43 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7383 (mp)
REVERT: B  118 ASP cc_start: 0.6004 (t70) cc_final: 0.5585 (t70)
REVERT: B  275 SER cc_start: 0.7967 (t) cc_final: 0.7387 (m)
  outliers start: 36
  outliers final: 32
  residues processed: 182
  average time/residue: 0.2460
  time to fit residues: 59.5094
Evaluate side-chains
  194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0670
   chunk 61 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6452
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8443  Z= 0.172
  Angle     :  0.577  14.500  11449  Z= 0.298
  Chirality :  0.043   0.175   1287
  Planarity :  0.004   0.060   1457
  Dihedral  :  4.448  20.852   1136
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.38 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1029
  helix:  1.46 (0.26), residues: 410
  sheet: -0.35 (0.35), residues: 212
  loop : -1.28 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 271 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.032   0.002   PHE R 194 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.007   0.000   ARG B  52 

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

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

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2058 Ramachandran restraints generated.
    1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 166
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.6769 (mtt180) cc_final: 0.6453 (mtt90)
REVERT: A  239 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7590 (t0)
REVERT: A  325 THR cc_start: 0.8057 (m) cc_final: 0.7822 (m)
REVERT: A  346 ARG cc_start: 0.6955 (mpp80) cc_final: 0.5890 (mtp85)
REVERT: B   43 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: B  118 ASP cc_start: 0.5966 (t70) cc_final: 0.5554 (t70)
REVERT: B  247 ASP cc_start: 0.7387 (p0) cc_final: 0.6884 (p0)
REVERT: B  275 SER cc_start: 0.7862 (t) cc_final: 0.7348 (m)
REVERT: G   42 GLU cc_start: 0.7240 (pp20) cc_final: 0.6978 (pp20)
  outliers start: 36
  outliers final: 30
  residues processed: 186
  average time/residue: 0.2284
  time to fit residues: 56.7353
Evaluate side-chains
  187 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  110 SER
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  123 ILE
Chi-restraints excluded: chain R residue  153 ILE
Chi-restraints excluded: chain R residue  177 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.231728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.197788 restraints weight = 8697.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 1.81
r_work: 0.4086 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3948 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8443  Z= 0.189
  Angle     :  0.596  13.938  11449  Z= 0.309
  Chirality :  0.044   0.203   1287
  Planarity :  0.004   0.059   1457
  Dihedral  :  4.484  21.002   1136
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.26 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.26), residues: 1029
  helix:  1.45 (0.26), residues: 410
  sheet: -0.34 (0.35), residues: 212
  loop : -1.29 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 271 
 HIS   0.008   0.001   HIS B  91 
 PHE   0.031   0.002   PHE R 194 
 TYR   0.013   0.001   TYR N  95 
 ARG   0.007   0.000   ARG B  52 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2159.70 seconds
wall clock time: 40 minutes 2.35 seconds (2402.35 seconds total)