Starting phenix.real_space_refine
on Sat May  2 20:25:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x5h_33014/05_2026/7x5h_33014.map"
  }
  resolution = 3.1
  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=   0.005 sd=   0.133
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      62      5.16       5
     C    5568      2.51       5
     N    1496      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8768
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1807
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 427
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "E"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1791
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2106
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 9, 'TRANS': 264}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 58
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'8K3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.93, per 1000 atoms: 0.22
  Number of scatterers: 8768
  At special positions: 0
  Unit cell: (118.881, 124.236, 106.029, 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      62     16.00
     O    1642      8.00
     N    1496      7.00
     C    5568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 192 " distance=2.00
    Simple disulfide: pdb=" SG  CYS R 311 " - pdb=" SG  CYS R 313 " 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: 0.75
  Conformation dependent library (CDL) restraints added in 329.7 milliseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      40.7% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.567A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.475A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 3.726A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.167A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.760A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.573A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    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 10 through 24
      removed outlier: 3.654A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.901A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.562A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.770A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 68
    Processing helix  chain 'R' and resid 69 through 72
    Processing helix  chain 'R' and resid 73 through 93
      removed outlier: 3.688A  pdb=" N   ASN R  77 " --> pdb=" O   ARG R  73 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU R  78 " --> pdb=" O   VAL R  74 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL R  79 " --> pdb=" O   PRO R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 93 through 103
      removed outlier: 3.801A  pdb=" N   SER R 103 " --> pdb=" O   VAL R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 110 through 145
      removed outlier: 3.676A  pdb=" N   GLN R 115 " --> pdb=" O   ARG R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 179
      removed outlier: 3.636A  pdb=" N   CYS R 156 " --> pdb=" O   ARG R 152 " (cutoff:3.500A)
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 197 through 209
      removed outlier: 3.611A  pdb=" N   PHE R 203 " --> pdb=" O   SER R 199 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 233
    Processing helix  chain 'R' and resid 277 through 311
      Proline residue:  R 300  - end of helix
      Proline residue:  R 309  - end of helix
    Processing helix  chain 'R' and resid 316 through 340
      removed outlier: 3.922A  pdb=" N   SER R 331 " --> pdb=" O   GLY R 327 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE R 332 " --> pdb=" O   TYR R 328 " (cutoff:3.500A)
      Proline residue:  R 335  - end of helix
    Processing helix  chain 'R' and resid 342 through 353
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.163A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52
      removed outlier: 5.353A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.917A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.581A  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: 4.419A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.103A  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: 6.852A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.967A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.111A  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: 6.559A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.820A  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: 3.739A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.697A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.697A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
      removed outlier: 3.575A  pdb=" N   VAL E 155 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.333A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1305 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: 1.51

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1432
        1.31 -     1.45: 2498
        1.45 -     1.58: 4935
        1.58 -     1.71: 0
        1.71 -     1.84: 88
  Bond restraints: 8953
  Sorted by residual:
  bond pdb=" C13 8K3 R 601 "
       pdb=" N15 8K3 R 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.458 -0.112 2.00e-02 2.50e+03 3.12e+01
  bond pdb=" C04 8K3 R 601 "
       pdb=" C08 8K3 R 601 "
    ideal  model  delta    sigma   weight residual
    1.435  1.532 -0.097 2.00e-02 2.50e+03 2.37e+01
  bond pdb=" C05 8K3 R 601 "
       pdb=" N06 8K3 R 601 "
    ideal  model  delta    sigma   weight residual
    1.371  1.318  0.053 2.00e-02 2.50e+03 6.90e+00
  bond pdb=" C10 8K3 R 601 "
       pdb=" C13 8K3 R 601 "
    ideal  model  delta    sigma   weight residual
    1.492  1.544 -0.052 2.00e-02 2.50e+03 6.83e+00
  bond pdb=" N   CYS R 114 "
       pdb=" CA  CYS R 114 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.25e+00
  ... (remaining 8948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 12015
        2.00 -     4.01: 103
        4.01 -     6.01: 13
        6.01 -     8.02: 0
        8.02 -    10.02: 2
  Bond angle restraints: 12133
  Sorted by residual:
  angle pdb=" N   VAL A 201 "
        pdb=" CA  VAL A 201 "
        pdb=" C   VAL A 201 "
      ideal   model   delta    sigma   weight residual
     112.17  108.64    3.53 9.50e-01 1.11e+00 1.38e+01
  angle pdb=" N   VAL E  64 "
        pdb=" CA  VAL E  64 "
        pdb=" C   VAL E  64 "
      ideal   model   delta    sigma   weight residual
     113.53  110.13    3.40 9.80e-01 1.04e+00 1.20e+01
  angle pdb=" C05 8K3 R 601 "
        pdb=" N06 8K3 R 601 "
        pdb=" C07 8K3 R 601 "
      ideal   model   delta    sigma   weight residual
     109.29  119.31  -10.02 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" N   CYS R 192 "
        pdb=" CA  CYS R 192 "
        pdb=" CB  CYS R 192 "
      ideal   model   delta    sigma   weight residual
     110.90  105.85    5.05 1.56e+00 4.11e-01 1.05e+01
  angle pdb=" N   CYS R 114 "
        pdb=" CA  CYS R 114 "
        pdb=" CB  CYS R 114 "
      ideal   model   delta    sigma   weight residual
     110.16  114.92   -4.76 1.48e+00 4.57e-01 1.03e+01
  ... (remaining 12128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4783
       17.94 -    35.88: 404
       35.88 -    53.81: 90
       53.81 -    71.75: 10
       71.75 -    89.69: 9
  Dihedral angle restraints: 5296
    sinusoidal: 2028
      harmonic: 3268
  Sorted by residual:
  dihedral pdb=" CA  CYS R 311 "
           pdb=" C   CYS R 311 "
           pdb=" N   SER R 312 "
           pdb=" CA  SER R 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.08   36.92     0      5.00e+00 4.00e-02 5.45e+01
  dihedral pdb=" CB  CYS R 311 "
           pdb=" SG  CYS R 311 "
           pdb=" SG  CYS R 313 "
           pdb=" CB  CYS R 313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.18  -37.82     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CB  GLU A  33 "
           pdb=" CG  GLU A  33 "
           pdb=" CD  GLU A  33 "
           pdb=" OE1 GLU A  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.69   89.69     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1115
       0.045 -    0.090: 179
       0.090 -    0.135: 71
       0.135 -    0.180: 3
       0.180 -    0.225: 1
  Chirality restraints: 1369
  Sorted by residual:
  chirality pdb=" CA  CYS R 192 "
            pdb=" N   CYS R 192 "
            pdb=" C   CYS R 192 "
            pdb=" CB  CYS R 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE R 315 "
            pdb=" N   ILE R 315 "
            pdb=" C   ILE R 315 "
            pdb=" CB  ILE R 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.18e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1366 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO B  39 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  54 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.46e+00
        pdb=" C   THR R  54 "    0.032 2.00e-02 2.50e+03
        pdb=" O   THR R  54 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PHE R  55 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 197 "    0.102 9.50e-02 1.11e+02   4.58e-02 1.47e+00
        pdb=" NE  ARG B 197 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 197 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 197 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 197 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 234
        2.70 -     3.25: 8787
        3.25 -     3.80: 13966
        3.80 -     4.35: 18269
        4.35 -     4.90: 31672
  Nonbonded interactions: 72928
  Sorted by model distance:
  nonbonded pdb=" O   SER A  44 "
            pdb=" ND2 ASN A 269 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" O   SER C  57 "
            pdb=" NH2 ARG C  62 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" NH1 ARG R 230 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" NH2 ARG B  46 "
            pdb=" OE2 GLU C  63 "
     model   vdw
     2.212 3.120
  ... (remaining 72923 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:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.470
  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:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
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      :  0.003   0.112   8955  Z= 0.156
  Angle     :  0.501  10.019  12137  Z= 0.275
  Chirality :  0.039   0.225   1369
  Planarity :  0.003   0.049   1537
  Dihedral  : 14.217  89.688   3180
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.26), residues: 1112
  helix:  3.55 (0.26), residues: 388
  sheet:  0.71 (0.29), residues: 284
  loop :  0.51 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 197 
 TYR   0.007   0.001   TYR E  60 
 PHE   0.008   0.001   PHE A 189 
 TRP   0.013   0.001   TRP R 325 
 HIS   0.002   0.000   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8953)
  covalent geometry    : angle       0.49180 (12133)
  SS BOND              : bond        0.02452 (    2)
  SS BOND              : angle       5.14670 (    4)
  hydrogen bonds       : bond        0.11592 (  460)
  hydrogen bonds       : angle       5.42159 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   58 ASN cc_start: 0.8378 (m110) cc_final: 0.8120 (m110)
REVERT: R  117 TRP cc_start: 0.7679 (t60) cc_final: 0.7459 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1198
  time to fit residues: 24.3036
Evaluate side-chains
  141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
E  39 GLN
E 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.187543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.133933 restraints weight = 10283.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.52
r_work: 0.3314 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8955  Z= 0.146
  Angle     :  0.521   6.466  12137  Z= 0.282
  Chirality :  0.042   0.159   1369
  Planarity :  0.004   0.045   1537
  Dihedral  :  4.075  31.163   1222
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.57 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.26), residues: 1112
  helix:  3.20 (0.26), residues: 394
  sheet:  0.47 (0.29), residues: 285
  loop :  0.37 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  62 
 TYR   0.015   0.001   TYR B 105 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8953)
  covalent geometry    : angle       0.52018 (12133)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       1.32666 (    4)
  hydrogen bonds       : bond        0.03690 (  460)
  hydrogen bonds       : angle       4.56656 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.370 
Fit side-chains
REVERT: B   61 MET cc_start: 0.8728 (ppp) cc_final: 0.8472 (ptm)
REVERT: B  264 TYR cc_start: 0.9003 (m-80) cc_final: 0.8582 (m-80)
REVERT: R   58 ASN cc_start: 0.8546 (m110) cc_final: 0.8264 (m110)
REVERT: R  141 TRP cc_start: 0.8459 (m100) cc_final: 0.8080 (m-10)
  outliers start: 8
  outliers final: 6
  residues processed: 151
  average time/residue: 0.1245
  time to fit residues: 24.5932
Evaluate side-chains
  143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 92 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0980
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 204 GLN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.186632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.128284 restraints weight = 10093.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.70
r_work: 0.3217 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8955  Z= 0.135
  Angle     :  0.496   6.392  12137  Z= 0.270
  Chirality :  0.041   0.166   1369
  Planarity :  0.003   0.042   1537
  Dihedral  :  4.127  28.745   1222
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.23 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.25), residues: 1112
  helix:  3.08 (0.26), residues: 394
  sheet:  0.44 (0.29), residues: 282
  loop :  0.16 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  48 
 TYR   0.017   0.001   TYR B 105 
 PHE   0.018   0.001   PHE R 203 
 TRP   0.011   0.001   TRP R 325 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8953)
  covalent geometry    : angle       0.49496 (12133)
  SS BOND              : bond        0.00544 (    2)
  SS BOND              : angle       1.42000 (    4)
  hydrogen bonds       : bond        0.03627 (  460)
  hydrogen bonds       : angle       4.38726 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: A  273 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7616 (tt)
REVERT: B   61 MET cc_start: 0.8863 (ppp) cc_final: 0.8569 (ptm)
REVERT: B  264 TYR cc_start: 0.9076 (m-80) cc_final: 0.8697 (m-80)
REVERT: E  220 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5739 (mp0)
REVERT: R   58 ASN cc_start: 0.8514 (m110) cc_final: 0.8262 (m110)
REVERT: R  141 TRP cc_start: 0.8477 (m100) cc_final: 0.7986 (m-10)
REVERT: R  276 ARG cc_start: 0.6107 (mmm-85) cc_final: 0.5459 (mtt-85)
  outliers start: 14
  outliers final: 7
  residues processed: 154
  average time/residue: 0.1246
  time to fit residues: 24.9205
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
E  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.186946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132762 restraints weight = 10353.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.65
r_work: 0.3298 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8955  Z= 0.113
  Angle     :  0.473   7.059  12137  Z= 0.258
  Chirality :  0.041   0.189   1369
  Planarity :  0.003   0.039   1537
  Dihedral  :  3.988  19.497   1222
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.19 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.25), residues: 1112
  helix:  3.13 (0.26), residues: 389
  sheet:  0.44 (0.29), residues: 284
  loop :  0.04 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 251 
 TYR   0.011   0.001   TYR B 105 
 PHE   0.018   0.001   PHE R 203 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8953)
  covalent geometry    : angle       0.47222 (12133)
  SS BOND              : bond        0.00602 (    2)
  SS BOND              : angle       1.11933 (    4)
  hydrogen bonds       : bond        0.03406 (  460)
  hydrogen bonds       : angle       4.32234 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7684 (tt)
REVERT: B  264 TYR cc_start: 0.9030 (m-80) cc_final: 0.8690 (m-80)
REVERT: C   21 MET cc_start: 0.8168 (mmm) cc_final: 0.7233 (tmm)
REVERT: E   82 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7674 (tp-100)
REVERT: E  220 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5867 (mp0)
REVERT: R  141 TRP cc_start: 0.8497 (m100) cc_final: 0.8065 (m-10)
REVERT: R  276 ARG cc_start: 0.6299 (mmm-85) cc_final: 0.5545 (mtt-85)
  outliers start: 16
  outliers final: 8
  residues processed: 163
  average time/residue: 0.1227
  time to fit residues: 26.1528
Evaluate side-chains
  155 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0070
   chunk 52 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 91 optimal weight:    8.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
E  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.187196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.132508 restraints weight = 10277.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.74
r_work: 0.3317 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8955  Z= 0.109
  Angle     :  0.473   6.889  12137  Z= 0.258
  Chirality :  0.041   0.197   1369
  Planarity :  0.003   0.039   1537
  Dihedral  :  3.910  19.349   1222
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.40 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.26), residues: 1112
  helix:  3.13 (0.26), residues: 389
  sheet:  0.37 (0.28), residues: 289
  loop :  0.02 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 251 
 TYR   0.009   0.001   TYR E  60 
 PHE   0.018   0.001   PHE R 203 
 TRP   0.024   0.001   TRP R 325 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8953)
  covalent geometry    : angle       0.47297 (12133)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       0.56187 (    4)
  hydrogen bonds       : bond        0.03319 (  460)
  hydrogen bonds       : angle       4.26014 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8784 (tt)
REVERT: A  273 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7728 (tt)
REVERT: B  264 TYR cc_start: 0.9014 (m-80) cc_final: 0.8652 (m-80)
REVERT: B  322 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8229 (m-30)
REVERT: C   21 MET cc_start: 0.8134 (mmm) cc_final: 0.7215 (tmm)
REVERT: E   82 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7577 (tp-100)
REVERT: E  220 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5925 (mp0)
REVERT: R  141 TRP cc_start: 0.8489 (m100) cc_final: 0.8078 (m-10)
REVERT: R  276 ARG cc_start: 0.6355 (mmm-85) cc_final: 0.5565 (mtt-85)
  outliers start: 22
  outliers final: 14
  residues processed: 162
  average time/residue: 0.1199
  time to fit residues: 25.4285
Evaluate side-chains
  163 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0770
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 71 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B  32 GLN
B 176 GLN
E  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.179539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126155 restraints weight = 10284.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.43
r_work: 0.3151 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8955  Z= 0.104
  Angle     :  0.467   7.066  12137  Z= 0.255
  Chirality :  0.040   0.212   1369
  Planarity :  0.003   0.037   1537
  Dihedral  :  3.852  19.135   1222
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.36 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.26), residues: 1112
  helix:  3.15 (0.26), residues: 388
  sheet:  0.25 (0.28), residues: 284
  loop : -0.09 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.009   0.001   TYR E  60 
 PHE   0.018   0.001   PHE R 203 
 TRP   0.033   0.001   TRP R 325 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8953)
  covalent geometry    : angle       0.46710 (12133)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       0.36365 (    4)
  hydrogen bonds       : bond        0.03272 (  460)
  hydrogen bonds       : angle       4.18261 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (tt)
REVERT: B  264 TYR cc_start: 0.9006 (m-80) cc_final: 0.8600 (m-80)
REVERT: E   43 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8495 (mmmm)
REVERT: E   82 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7486 (tp-100)
REVERT: E  220 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5895 (mp0)
REVERT: R   58 ASN cc_start: 0.8331 (m110) cc_final: 0.8075 (m110)
REVERT: R  141 TRP cc_start: 0.8420 (m100) cc_final: 0.7990 (m-10)
REVERT: R  276 ARG cc_start: 0.6308 (mmm-85) cc_final: 0.5506 (mtt-85)
  outliers start: 21
  outliers final: 15
  residues processed: 163
  average time/residue: 0.1195
  time to fit residues: 25.4993
Evaluate side-chains
  161 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  194 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:   30.0000
   chunk 64 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 56 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.174399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.115011 restraints weight = 10417.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.45
r_work: 0.3024 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8955  Z= 0.215
  Angle     :  0.563   7.192  12137  Z= 0.303
  Chirality :  0.043   0.219   1369
  Planarity :  0.004   0.035   1537
  Dihedral  :  4.335  21.612   1222
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.36 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.25), residues: 1112
  helix:  2.90 (0.26), residues: 392
  sheet:  0.09 (0.28), residues: 285
  loop : -0.18 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 160 
 TYR   0.016   0.002   TYR B 105 
 PHE   0.017   0.002   PHE R 203 
 TRP   0.032   0.002   TRP R 325 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 8953)
  covalent geometry    : angle       0.56308 (12133)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.55055 (    4)
  hydrogen bonds       : bond        0.03947 (  460)
  hydrogen bonds       : angle       4.41025 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8831 (tt)
REVERT: B  264 TYR cc_start: 0.9141 (m-80) cc_final: 0.8631 (m-80)
REVERT: B  273 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8540 (mm)
REVERT: C   58 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7627 (mp0)
REVERT: E   43 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8400 (mmmm)
REVERT: R   58 ASN cc_start: 0.8390 (m110) cc_final: 0.8045 (m110)
REVERT: R  141 TRP cc_start: 0.8415 (m100) cc_final: 0.7871 (m-10)
REVERT: R  276 ARG cc_start: 0.6303 (mmm-85) cc_final: 0.5378 (mtt-85)
  outliers start: 26
  outliers final: 17
  residues processed: 164
  average time/residue: 0.1244
  time to fit residues: 26.4670
Evaluate side-chains
  162 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  111 ARG
Chi-restraints excluded: chain R residue  194 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 90 optimal weight:   20.0000
   chunk 55 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.176634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117520 restraints weight = 10297.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.46
r_work: 0.3149 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8955  Z= 0.130
  Angle     :  0.503   7.169  12137  Z= 0.272
  Chirality :  0.041   0.230   1369
  Planarity :  0.003   0.034   1537
  Dihedral  :  4.106  20.937   1222
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.64 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.25), residues: 1112
  helix:  3.08 (0.26), residues: 385
  sheet:  0.10 (0.28), residues: 286
  loop : -0.16 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 111 
 TYR   0.009   0.001   TYR B 105 
 PHE   0.016   0.001   PHE R 203 
 TRP   0.033   0.001   TRP R 325 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8953)
  covalent geometry    : angle       0.50260 (12133)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       0.41556 (    4)
  hydrogen bonds       : bond        0.03532 (  460)
  hydrogen bonds       : angle       4.29092 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8824 (tt)
REVERT: B  264 TYR cc_start: 0.9034 (m-80) cc_final: 0.8660 (m-80)
REVERT: B  273 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8501 (mm)
REVERT: E   39 GLN cc_start: 0.8822 (tt0) cc_final: 0.8464 (tt0)
REVERT: R   58 ASN cc_start: 0.8347 (m110) cc_final: 0.7980 (m110)
REVERT: R  141 TRP cc_start: 0.8449 (m100) cc_final: 0.7982 (m-10)
REVERT: R  276 ARG cc_start: 0.6473 (mmm-85) cc_final: 0.5822 (mtt-85)
  outliers start: 22
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1190
  time to fit residues: 23.1916
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  194 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 71 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 86 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0030
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.176148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.117037 restraints weight = 10250.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.45
r_work: 0.3117 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8955  Z= 0.111
  Angle     :  0.488   7.133  12137  Z= 0.264
  Chirality :  0.041   0.236   1369
  Planarity :  0.003   0.037   1537
  Dihedral  :  3.973  20.249   1222
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.64 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.25), residues: 1112
  helix:  2.96 (0.26), residues: 395
  sheet:  0.13 (0.28), residues: 289
  loop : -0.19 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 197 
 TYR   0.010   0.001   TYR E  60 
 PHE   0.016   0.001   PHE R 203 
 TRP   0.030   0.001   TRP R 325 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8953)
  covalent geometry    : angle       0.48806 (12133)
  SS BOND              : bond        0.00105 (    2)
  SS BOND              : angle       0.38264 (    4)
  hydrogen bonds       : bond        0.03347 (  460)
  hydrogen bonds       : angle       4.21800 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8791 (tt)
REVERT: B  264 TYR cc_start: 0.9004 (m-80) cc_final: 0.8647 (m-80)
REVERT: B  273 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8470 (mm)
REVERT: R   58 ASN cc_start: 0.8323 (m110) cc_final: 0.7969 (m110)
REVERT: R  141 TRP cc_start: 0.8449 (m100) cc_final: 0.7998 (m-10)
REVERT: R  276 ARG cc_start: 0.6460 (mmm-85) cc_final: 0.5874 (mtt-85)
  outliers start: 23
  outliers final: 18
  residues processed: 147
  average time/residue: 0.1214
  time to fit residues: 23.3468
Evaluate side-chains
  154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  194 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 102 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
B 239 ASN
E 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.175033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.129523 restraints weight = 10302.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 3.22
r_work: 0.3068 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8955  Z= 0.149
  Angle     :  0.518   7.093  12137  Z= 0.280
  Chirality :  0.042   0.239   1369
  Planarity :  0.003   0.036   1537
  Dihedral  :  4.071  20.926   1222
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.06 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.25), residues: 1112
  helix:  2.89 (0.26), residues: 395
  sheet:  0.03 (0.28), residues: 297
  loop : -0.17 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.010   0.001   TYR B 105 
 PHE   0.014   0.001   PHE R 203 
 TRP   0.028   0.001   TRP R 325 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8953)
  covalent geometry    : angle       0.51800 (12133)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.39269 (    4)
  hydrogen bonds       : bond        0.03576 (  460)
  hydrogen bonds       : angle       4.25924 ( 1305)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8766 (tt)
REVERT: B  273 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8397 (mm)
REVERT: R   58 ASN cc_start: 0.8335 (m110) cc_final: 0.7947 (m110)
REVERT: R  141 TRP cc_start: 0.8459 (m100) cc_final: 0.8042 (m-10)
REVERT: R  276 ARG cc_start: 0.6581 (mmm-85) cc_final: 0.6020 (mtt-85)
  outliers start: 24
  outliers final: 18
  residues processed: 147
  average time/residue: 0.1206
  time to fit residues: 23.2127
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain E residue   78 THR
Chi-restraints excluded: chain E residue  219 LEU
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  194 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0970
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 90 optimal weight:   20.0000
   chunk 30 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0570
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.178628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133224 restraints weight = 10313.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 3.17
r_work: 0.3111 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8955  Z= 0.102
  Angle     :  0.494   8.042  12137  Z= 0.264
  Chirality :  0.041   0.239   1369
  Planarity :  0.003   0.035   1537
  Dihedral  :  3.877  19.797   1222
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.17 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.25), residues: 1112
  helix:  3.17 (0.26), residues: 386
  sheet:  0.17 (0.28), residues: 284
  loop : -0.20 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.010   0.001   TYR E  60 
 PHE   0.015   0.001   PHE R 203 
 TRP   0.029   0.001   TRP R 325 
 HIS   0.003   0.000   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8953)
  covalent geometry    : angle       0.49403 (12133)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.35598 (    4)
  hydrogen bonds       : bond        0.03218 (  460)
  hydrogen bonds       : angle       4.18033 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2915.37 seconds
wall clock time: 50 minutes 35.16 seconds (3035.16 seconds total)