Starting phenix.real_space_refine
on Thu Jul  2 14:18:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vje_65110/07_2026/9vje_65110.cif"
  }
  resolution = 2.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.074
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      60      5.16       5
     C    5552      2.51       5
     N    1472      2.21       5
     O    1612      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8698
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1680
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 211}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 2556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2556
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 399
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "E"
      Number of atoms: 1781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1781
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 2167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2167
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 264}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 115
          Unusual residues: {'CLR': 2, 'T7M': 1, 'YLX': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'T7M:plan-3': 1, 'T7M:plan-4': 1, 'T7M:plan-5': 1, 'T7M:plan-6': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 2.36, per 1000 atoms: 0.27
  Number of scatterers: 8698
  At special positions: 0
  Unit cell: (87.74, 116.44, 127.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       2     15.00
     O    1612      8.00
     N    1472      7.00
     C    5552      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 109 " - pdb=" SG  CYS R 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 371 " - pdb=" SG  CYS R 375 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 614.5 milliseconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      39.9% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 208 through 217
      removed outlier: 3.872A  pdb=" N   ILE B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   HIS B 214 " --> pdb=" O   LYS B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 256
    Processing helix  chain 'B' and resid 257 through 261
      removed outlier: 3.853A  pdb=" N   ILE B 261 " --> pdb=" O   LYS B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 282
      removed outlier: 3.624A  pdb=" N   LYS B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 310
    Processing helix  chain 'B' and resid 330 through 352
    Processing helix  chain 'C' and resid 8 through 26
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 35 through 37
      No H-bonds generated for 'chain 'C' and resid 35 through 37'
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 208 through 212
      removed outlier: 3.572A  pdb=" N   VAL E 212 " --> pdb=" O   ALA E 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 64
    Processing helix  chain 'R' and resid 65 through 68
    Processing helix  chain 'R' and resid 69 through 89
    Processing helix  chain 'R' and resid 89 through 100
    Processing helix  chain 'R' and resid 106 through 140
    Processing helix  chain 'R' and resid 140 through 147
    Processing helix  chain 'R' and resid 149 through 173
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 192 through 202
    Processing helix  chain 'R' and resid 204 through 230
    Processing helix  chain 'R' and resid 330 through 368
      Proline residue:  R 360  - end of helix
    Processing helix  chain 'R' and resid 369 through 371
      No H-bonds generated for 'chain 'R' and resid 369 through 371'
    Processing helix  chain 'R' and resid 378 through 401
      removed outlier: 4.008A  pdb=" N   GLY R 389 " --> pdb=" O   ILE R 385 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TYR R 390 " --> pdb=" O   ASN R 386 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
    Processing helix  chain 'R' and resid 404 through 414
    Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192
      removed outlier: 6.238A  pdb=" N   VAL B  34 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ALA B 221 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE B 222 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   PHE B 268 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   PHE B 224 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ASN B 270 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL B 226 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE B 265 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   HIS B 322 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU B 267 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.458A  pdb=" N   THR C  47 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ASN C 340 " --> pdb=" O   THR C  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.919A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 5.882A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.771A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.812A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.653A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.382A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.142A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 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: 6.607A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.364A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    475 hydrogen bonds defined for protein.
    1320 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: 1.49

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2778
        1.34 -     1.46: 1956
        1.46 -     1.58: 4059
        1.58 -     1.70: 1
        1.70 -     1.82: 87
  Bond restraints: 8881
  Sorted by residual:
  bond pdb=" O4  T7M R 504 "
       pdb=" P4  T7M R 504 "
    ideal  model  delta    sigma   weight residual
    1.704  1.824 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" C4  T7M R 504 "
       pdb=" O4  T7M R 504 "
    ideal  model  delta    sigma   weight residual
    1.402  1.327  0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" O13 T7M R 504 "
       pdb=" P1  T7M R 504 "
    ideal  model  delta    sigma   weight residual
    1.659  1.713 -0.054 2.00e-02 2.50e+03 7.28e+00
  bond pdb=" C4  T7M R 504 "
       pdb=" C5  T7M R 504 "
    ideal  model  delta    sigma   weight residual
    1.527  1.579 -0.052 2.00e-02 2.50e+03 6.65e+00
  bond pdb=" C7  T7M R 504 "
       pdb=" O13 T7M R 504 "
    ideal  model  delta    sigma   weight residual
    1.411  1.365  0.046 2.00e-02 2.50e+03 5.39e+00
  ... (remaining 8876 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.94: 12006
        3.94 -     7.89: 50
        7.89 -    11.83: 2
       11.83 -    15.77: 0
       15.77 -    19.72: 1
  Bond angle restraints: 12059
  Sorted by residual:
  angle pdb=" C   GLU E 222 "
        pdb=" N   TYR E 223 "
        pdb=" CA  TYR E 223 "
      ideal   model   delta    sigma   weight residual
     121.80  102.08   19.72 2.44e+00 1.68e-01 6.53e+01
  angle pdb=" N   TYR E 223 "
        pdb=" CA  TYR E 223 "
        pdb=" C   TYR E 223 "
      ideal   model   delta    sigma   weight residual
     109.81  101.10    8.71 2.21e+00 2.05e-01 1.55e+01
  angle pdb=" N   GLU E 222 "
        pdb=" CA  GLU E 222 "
        pdb=" C   GLU E 222 "
      ideal   model   delta    sigma   weight residual
     110.53  106.02    4.51 1.29e+00 6.01e-01 1.22e+01
  angle pdb=" CA  TYR E 178 "
        pdb=" CB  TYR E 178 "
        pdb=" CG  TYR E 178 "
      ideal   model   delta    sigma   weight residual
     113.90  118.78   -4.88 1.80e+00 3.09e-01 7.35e+00
  angle pdb=" CB  MET D  38 "
        pdb=" CG  MET D  38 "
        pdb=" SD  MET D  38 "
      ideal   model   delta    sigma   weight residual
     112.70  104.76    7.94 3.00e+00 1.11e-01 7.00e+00
  ... (remaining 12054 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.39: 5309
       34.39 -    68.79: 89
       68.79 -   103.18: 12
      103.18 -   137.58: 1
      137.58 -   171.97: 3
  Dihedral angle restraints: 5414
    sinusoidal: 2195
      harmonic: 3219
  Sorted by residual:
  dihedral pdb=" CB  CYS E 147 "
           pdb=" SG  CYS E 147 "
           pdb=" SG  CYS E 217 "
           pdb=" CB  CYS E 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.31  -60.31     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" C10 T7M R 504 "
           pdb=" C8  T7M R 504 "
           pdb=" O16 T7M R 504 "
           pdb=" C7  T7M R 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.77 -116.20  171.97     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C10 T7M R 504 "
           pdb=" C8  T7M R 504 "
           pdb=" O16 T7M R 504 "
           pdb=" C9  T7M R 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.02  121.90  166.12     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1183
       0.068 -    0.136: 189
       0.136 -    0.204: 7
       0.204 -    0.271: 4
       0.271 -    0.339: 4
  Chirality restraints: 1387
  Sorted by residual:
  chirality pdb=" C3  T7M R 504 "
            pdb=" C2  T7M R 504 "
            pdb=" C4  T7M R 504 "
            pdb=" O3  T7M R 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.37    2.70   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" C14 CLR R 503 "
            pdb=" C13 CLR R 503 "
            pdb=" C15 CLR R 503 "
            pdb=" C8  CLR R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" C14 CLR R 502 "
            pdb=" C13 CLR R 502 "
            pdb=" C15 CLR R 502 "
            pdb=" C8  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.64    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1384 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" N   YLX R 501 "   -0.015 2.00e-02 2.50e+03   6.14e-02 5.66e+01
        pdb=" C   YLX R 501 "   -0.011 2.00e-02 2.50e+03
        pdb=" O   YLX R 501 "   -0.072 2.00e-02 2.50e+03
        pdb=" C1  YLX R 501 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  YLX R 501 "   -0.064 2.00e-02 2.50e+03
        pdb=" C9  YLX R 501 "    0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 223 "   -0.026 2.00e-02 2.50e+03   2.34e-02 1.09e+01
        pdb=" CG  TYR E 223 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 223 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 223 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 223 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 223 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 223 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR E 223 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  68 "   -0.009 2.00e-02 2.50e+03   1.58e-02 4.36e+00
        pdb=" CG  PHE E  68 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  68 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  68 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  68 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  68 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  68 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 118
        2.61 -     3.18: 7607
        3.18 -     3.75: 14957
        3.75 -     4.33: 21676
        4.33 -     4.90: 34346
  Nonbonded interactions: 78704
  Sorted by model distance:
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.033 3.040
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" NE2 GLN E 167 "
            pdb=" O   GLN E 171 "
     model   vdw
     2.102 3.120
  nonbonded pdb=" O   LEU R 166 "
            pdb=" OH  TYR R 198 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OG  SER C 147 "
            pdb=" O   VAL C 187 "
     model   vdw
     2.128 3.040
  ... (remaining 78699 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:             3.630
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     10.410
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
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      :  0.005   0.120   8884  Z= 0.235
  Angle     :  0.717  19.716  12065  Z= 0.370
  Chirality :  0.051   0.339   1387
  Planarity :  0.004   0.061   1504
  Dihedral  : 14.845 171.974   3329
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.25), residues: 1093
  helix:  1.60 (0.25), residues: 398
  sheet: -0.17 (0.31), residues: 269
  loop : -0.77 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  38 
 TYR   0.055   0.003   TYR E 223 
 PHE   0.034   0.002   PHE E  68 
 TRP   0.014   0.002   TRP C  99 
 HIS   0.006   0.001   HIS B 245 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00523 /  0.24 ( 8881)
  covalent geometry    : angle       0.71749 /  0.37 (12059)
  SS BOND              : bond        0.00420 /  0.22 (    3)
  SS BOND              : angle       0.72993 /  0.36 (    6)
  hydrogen bonds       : bond        0.16828 / 10.99 (  475)
  hydrogen bonds       : angle       7.15140 /  5.02 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.344 
Fit side-chains
REVERT: R  100 ASN cc_start: 0.7756 (t0) cc_final: 0.7473 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.6243
  time to fit residues: 93.4508
Evaluate side-chains
  119 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0170
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
B 316 ASN
C 156 GLN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN
R  54 ASN
R  72 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.174181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141328 restraints weight = 8682.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.47
r_work: 0.3498 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
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   0.051   8884  Z= 0.156
  Angle     :  0.617  10.537  12065  Z= 0.323
  Chirality :  0.044   0.154   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 11.194 178.608   1422
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  8.71 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.26), residues: 1093
  helix:  2.07 (0.25), residues: 401
  sheet: -0.27 (0.31), residues: 257
  loop : -0.61 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  22 
 TYR   0.029   0.002   TYR E 223 
 PHE   0.015   0.002   PHE E  68 
 TRP   0.018   0.002   TRP C 339 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 8881)
  covalent geometry    : angle       0.61679 /  0.32 (12059)
  SS BOND              : bond        0.00177 /  0.09 (    3)
  SS BOND              : angle       0.56626 /  0.32 (    6)
  hydrogen bonds       : bond        0.04746 /  3.06 (  475)
  hydrogen bonds       : angle       5.68324 /  3.98 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.318 
Fit side-chains
REVERT: E  154 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7962 (tp)
REVERT: R  100 ASN cc_start: 0.8158 (t0) cc_final: 0.7586 (t0)
REVERT: R  341 ARG cc_start: 0.6867 (mmp-170) cc_final: 0.6648 (mmp-170)
REVERT: R  405 LYS cc_start: 0.7520 (tppp) cc_final: 0.7107 (tppt)
  outliers start: 14
  outliers final: 5
  residues processed: 130
  average time/residue: 0.6406
  time to fit residues: 88.0536
Evaluate side-chains
  121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  185 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
C 156 GLN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.173717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139743 restraints weight = 8577.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.66
r_work: 0.3480 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8884  Z= 0.162
  Angle     :  0.598   9.787  12065  Z= 0.311
  Chirality :  0.043   0.143   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.660 174.917   1422
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.21 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.74 (0.26), residues: 1093
  helix:  2.28 (0.25), residues: 400
  sheet: -0.33 (0.31), residues: 257
  loop : -0.64 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  22 
 TYR   0.019   0.002   TYR E 178 
 PHE   0.019   0.002   PHE R 361 
 TRP   0.015   0.002   TRP C 339 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 8881)
  covalent geometry    : angle       0.59813 /  0.31 (12059)
  SS BOND              : bond        0.00236 /  0.12 (    3)
  SS BOND              : angle       0.69982 /  0.40 (    6)
  hydrogen bonds       : bond        0.04486 /  2.90 (  475)
  hydrogen bonds       : angle       5.46430 /  3.82 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: D   42 GLU cc_start: 0.7914 (pt0) cc_final: 0.7084 (mm-30)
REVERT: D   47 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7469 (pt0)
REVERT: E   46 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6615 (tm-30)
REVERT: R  341 ARG cc_start: 0.6761 (mmt180) cc_final: 0.6500 (mmp-170)
  outliers start: 21
  outliers final: 9
  residues processed: 129
  average time/residue: 0.6808
  time to fit residues: 92.6276
Evaluate side-chains
  125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 103 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 72 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.174028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140382 restraints weight = 8799.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.53
r_work: 0.3483 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8884  Z= 0.157
  Angle     :  0.589  10.208  12065  Z= 0.305
  Chirality :  0.043   0.143   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.469 173.476   1422
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.06 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.74 (0.26), residues: 1093
  helix:  2.36 (0.25), residues: 396
  sheet: -0.37 (0.31), residues: 257
  loop : -0.67 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  22 
 TYR   0.018   0.002   TYR E 178 
 PHE   0.017   0.002   PHE R 361 
 TRP   0.014   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 8881)
  covalent geometry    : angle       0.58932 /  0.30 (12059)
  SS BOND              : bond        0.00215 /  0.11 (    3)
  SS BOND              : angle       0.68320 /  0.39 (    6)
  hydrogen bonds       : bond        0.04257 /  2.75 (  475)
  hydrogen bonds       : angle       5.36958 /  3.75 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: C  214 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6912 (mmt180)
REVERT: D   42 GLU cc_start: 0.7868 (pt0) cc_final: 0.7078 (mm-30)
REVERT: E   46 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6725 (tm-30)
REVERT: E  154 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7979 (tp)
REVERT: E  223 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6217 (t80)
REVERT: R  341 ARG cc_start: 0.6666 (mmt180) cc_final: 0.6432 (mmp-170)
  outliers start: 24
  outliers final: 11
  residues processed: 133
  average time/residue: 0.6907
  time to fit residues: 96.9279
Evaluate side-chains
  133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  189 ILE
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.173633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140116 restraints weight = 8700.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.60
r_work: 0.3479 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8884  Z= 0.166
  Angle     :  0.604  13.499  12065  Z= 0.309
  Chirality :  0.043   0.144   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.366 173.926   1422
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.82 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.70 (0.26), residues: 1093
  helix:  2.37 (0.25), residues: 395
  sheet: -0.45 (0.31), residues: 259
  loop : -0.69 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 223 
 TYR   0.020   0.002   TYR E 178 
 PHE   0.020   0.002   PHE E  68 
 TRP   0.012   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.17 ( 8881)
  covalent geometry    : angle       0.60410 /  0.31 (12059)
  SS BOND              : bond        0.00262 /  0.14 (    3)
  SS BOND              : angle       0.72728 /  0.41 (    6)
  hydrogen bonds       : bond        0.04277 /  2.76 (  475)
  hydrogen bonds       : angle       5.37079 /  3.76 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.377 
Fit side-chains
REVERT: C  214 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6984 (mmt180)
REVERT: D   42 GLU cc_start: 0.7889 (pt0) cc_final: 0.7129 (mm-30)
REVERT: D   47 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7294 (pt0)
REVERT: E   46 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6663 (tm-30)
REVERT: E  223 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6427 (t80)
REVERT: R  209 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7581 (tp)
REVERT: R  341 ARG cc_start: 0.6709 (mmt180) cc_final: 0.6465 (mmp-170)
REVERT: R  405 LYS cc_start: 0.7512 (tppp) cc_final: 0.7023 (tppt)
  outliers start: 27
  outliers final: 11
  residues processed: 133
  average time/residue: 0.7025
  time to fit residues: 98.6670
Evaluate side-chains
  133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  189 ILE
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
C 156 GLN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139849 restraints weight = 8656.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.50
r_work: 0.3474 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8884  Z= 0.176
  Angle     :  0.615  12.828  12065  Z= 0.314
  Chirality :  0.043   0.144   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.297 174.493   1422
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.49 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.66 (0.26), residues: 1093
  helix:  2.31 (0.25), residues: 395
  sheet: -0.46 (0.31), residues: 259
  loop : -0.70 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 223 
 TYR   0.021   0.002   TYR E 178 
 PHE   0.023   0.002   PHE E  68 
 TRP   0.012   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.18 ( 8881)
  covalent geometry    : angle       0.61538 /  0.31 (12059)
  SS BOND              : bond        0.00288 /  0.15 (    3)
  SS BOND              : angle       0.76109 /  0.43 (    6)
  hydrogen bonds       : bond        0.04332 /  2.79 (  475)
  hydrogen bonds       : angle       5.39077 /  3.77 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.348 
Fit side-chains
REVERT: C  214 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6977 (mmt180)
REVERT: D   42 GLU cc_start: 0.7829 (pt0) cc_final: 0.7086 (mm-30)
REVERT: D   47 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7329 (pt0)
REVERT: E   46 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6691 (tm-30)
REVERT: E  154 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: E  223 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6581 (t80)
REVERT: R  209 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7599 (tp)
REVERT: R  217 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7955 (mtm-85)
REVERT: R  341 ARG cc_start: 0.6704 (mmt180) cc_final: 0.6491 (mmt180)
REVERT: R  405 LYS cc_start: 0.7542 (tppp) cc_final: 0.7034 (tppt)
  outliers start: 30
  outliers final: 17
  residues processed: 133
  average time/residue: 0.6951
  time to fit residues: 97.6959
Evaluate side-chains
  143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  189 ILE
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  217 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 97 optimal weight:    0.1980
   chunk 95 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141099 restraints weight = 8709.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 1.52
r_work: 0.3489 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8884  Z= 0.155
  Angle     :  0.601  12.487  12065  Z= 0.305
  Chirality :  0.043   0.144   1387
  Planarity :  0.004   0.048   1504
  Dihedral  : 10.136 174.048   1422
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.36 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.70 (0.26), residues: 1093
  helix:  2.36 (0.25), residues: 395
  sheet: -0.43 (0.31), residues: 257
  loop : -0.70 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  22 
 TYR   0.019   0.002   TYR E 178 
 PHE   0.026   0.002   PHE E  68 
 TRP   0.013   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 8881)
  covalent geometry    : angle       0.60053 /  0.31 (12059)
  SS BOND              : bond        0.00222 /  0.12 (    3)
  SS BOND              : angle       0.67875 /  0.39 (    6)
  hydrogen bonds       : bond        0.04165 /  2.69 (  475)
  hydrogen bonds       : angle       5.31600 /  3.72 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 0.392 
Fit side-chains
REVERT: C  214 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6987 (mmt180)
REVERT: D   42 GLU cc_start: 0.7781 (pt0) cc_final: 0.7054 (mm-30)
REVERT: E   46 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6677 (tm-30)
REVERT: E  154 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: E  223 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.6613 (t80)
REVERT: R  209 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7557 (tp)
REVERT: R  217 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7960 (mtm-85)
REVERT: R  341 ARG cc_start: 0.6667 (mmt180) cc_final: 0.6372 (mmp-170)
REVERT: R  405 LYS cc_start: 0.7487 (tppp) cc_final: 0.6976 (tppt)
  outliers start: 30
  outliers final: 16
  residues processed: 137
  average time/residue: 0.6562
  time to fit residues: 95.1982
Evaluate side-chains
  139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  217 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 85 optimal weight:    0.2980
   chunk 90 optimal weight:    0.5980
   chunk 81 optimal weight:    4.9990
   chunk 32 optimal weight:    0.4980
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.176860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.143596 restraints weight = 8669.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.52
r_work: 0.3518 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8884  Z= 0.134
  Angle     :  0.589  12.080  12065  Z= 0.298
  Chirality :  0.042   0.175   1387
  Planarity :  0.004   0.049   1504
  Dihedral  :  9.948 174.088   1422
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.43 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.74 (0.26), residues: 1093
  helix:  2.38 (0.25), residues: 395
  sheet: -0.44 (0.31), residues: 261
  loop : -0.65 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  46 
 TYR   0.018   0.002   TYR E 178 
 PHE   0.023   0.002   PHE E  68 
 TRP   0.014   0.002   TRP C 339 
 HIS   0.004   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 8881)
  covalent geometry    : angle       0.58923 /  0.30 (12059)
  SS BOND              : bond        0.00163 /  0.09 (    3)
  SS BOND              : angle       0.55536 /  0.31 (    6)
  hydrogen bonds       : bond        0.04010 /  2.59 (  475)
  hydrogen bonds       : angle       5.22952 /  3.64 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.354 
Fit side-chains
REVERT: B  323 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7026 (mpp)
REVERT: C  214 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6907 (mmt180)
REVERT: D   42 GLU cc_start: 0.7745 (pt0) cc_final: 0.7048 (mm-30)
REVERT: E  154 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8035 (tp)
REVERT: E  223 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6508 (t80)
REVERT: R  209 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7534 (tp)
REVERT: R  341 ARG cc_start: 0.6656 (mmt180) cc_final: 0.6363 (mmp-170)
REVERT: R  405 LYS cc_start: 0.7465 (tppp) cc_final: 0.6959 (tppt)
  outliers start: 21
  outliers final: 14
  residues processed: 133
  average time/residue: 0.6460
  time to fit residues: 91.2028
Evaluate side-chains
  134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  323 MET
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 104 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
B 331 ASN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.175104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141605 restraints weight = 8650.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.52
r_work: 0.3497 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8884  Z= 0.156
  Angle     :  0.614  12.260  12065  Z= 0.310
  Chirality :  0.043   0.187   1387
  Planarity :  0.004   0.048   1504
  Dihedral  :  9.904 174.718   1422
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.89 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.68 (0.26), residues: 1093
  helix:  2.36 (0.25), residues: 395
  sheet: -0.51 (0.31), residues: 263
  loop : -0.68 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  46 
 TYR   0.019   0.002   TYR E 178 
 PHE   0.025   0.002   PHE E  68 
 TRP   0.012   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 ( 8881)
  covalent geometry    : angle       0.61424 /  0.31 (12059)
  SS BOND              : bond        0.00260 /  0.14 (    3)
  SS BOND              : angle       0.67640 /  0.38 (    6)
  hydrogen bonds       : bond        0.04143 /  2.67 (  475)
  hydrogen bonds       : angle       5.26572 /  3.67 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.356 
Fit side-chains
REVERT: C  214 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6927 (mmt180)
REVERT: C  226 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7783 (pm20)
REVERT: D   21 MET cc_start: 0.6129 (mtm) cc_final: 0.5624 (ptm)
REVERT: D   42 GLU cc_start: 0.7747 (pt0) cc_final: 0.7090 (mm-30)
REVERT: E   46 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6664 (tm-30)
REVERT: E  154 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8050 (tp)
REVERT: E  223 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6589 (t80)
REVERT: R  209 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7554 (tp)
REVERT: R  341 ARG cc_start: 0.6689 (mmt180) cc_final: 0.6476 (mmt180)
REVERT: R  405 LYS cc_start: 0.7476 (tppp) cc_final: 0.6963 (tppt)
  outliers start: 27
  outliers final: 16
  residues processed: 131
  average time/residue: 0.6782
  time to fit residues: 94.1079
Evaluate side-chains
  137 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 58 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9990
   chunk 99 optimal weight:    0.5980
   chunk 95 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.176162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143230 restraints weight = 8696.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.53
r_work: 0.3514 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8884  Z= 0.142
  Angle     :  0.607  12.207  12065  Z= 0.305
  Chirality :  0.043   0.181   1387
  Planarity :  0.004   0.049   1504
  Dihedral  :  9.648 174.816   1422
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.10 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.70 (0.26), residues: 1093
  helix:  2.37 (0.25), residues: 395
  sheet: -0.45 (0.31), residues: 260
  loop : -0.71 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  46 
 TYR   0.018   0.002   TYR E 178 
 PHE   0.024   0.002   PHE E  68 
 TRP   0.013   0.002   TRP C 339 
 HIS   0.003   0.001   HIS E  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 8881)
  covalent geometry    : angle       0.60680 /  0.31 (12059)
  SS BOND              : bond        0.00216 /  0.11 (    3)
  SS BOND              : angle       0.66159 /  0.38 (    6)
  hydrogen bonds       : bond        0.04051 /  2.61 (  475)
  hydrogen bonds       : angle       5.21584 /  3.63 ( 1320)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.334 
Fit side-chains
REVERT: C  214 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6915 (mmt180)
REVERT: C  226 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7763 (pm20)
REVERT: C  262 MET cc_start: 0.8943 (tpp) cc_final: 0.8722 (mmt)
REVERT: D   21 MET cc_start: 0.6031 (mtm) cc_final: 0.5572 (ptm)
REVERT: D   42 GLU cc_start: 0.7758 (pt0) cc_final: 0.7089 (mm-30)
REVERT: E   46 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6667 (tm-30)
REVERT: E  154 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8071 (tp)
REVERT: E  223 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6578 (t80)
REVERT: R  209 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7540 (tp)
REVERT: R  341 ARG cc_start: 0.6690 (mmt180) cc_final: 0.6478 (mmt180)
REVERT: R  405 LYS cc_start: 0.7474 (tppp) cc_final: 0.6965 (tppt)
  outliers start: 24
  outliers final: 18
  residues processed: 129
  average time/residue: 0.6699
  time to fit residues: 91.5740
Evaluate side-chains
  135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain B residue  326 SER
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  226 GLU
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  146 SER
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 TYR
Chi-restraints excluded: chain R residue  189 ILE
Chi-restraints excluded: chain R residue  196 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  210 LEU
Chi-restraints excluded: chain R residue  340 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 196 HIS
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.174464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.140704 restraints weight = 8600.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 1.52
r_work: 0.3485 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8884  Z= 0.171
  Angle     :  0.634  12.385  12065  Z= 0.319
  Chirality :  0.043   0.170   1387
  Planarity :  0.004   0.048   1504
  Dihedral  :  9.651 174.865   1422
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.65 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    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:  0.62 (0.26), residues: 1093
  helix:  2.29 (0.25), residues: 395
  sheet: -0.49 (0.31), residues: 261
  loop : -0.73 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  46 
 TYR   0.021   0.002   TYR E 178 
 PHE   0.027   0.002   PHE E  68 
 TRP   0.011   0.002   TRP C 339 
 HIS   0.003   0.001   HIS C  62 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.17 ( 8881)
  covalent geometry    : angle       0.63366 /  0.32 (12059)
  SS BOND              : bond        0.00326 /  0.17 (    3)
  SS BOND              : angle       0.77858 /  0.44 (    6)
  hydrogen bonds       : bond        0.04263 /  2.74 (  475)
  hydrogen bonds       : angle       5.30663 /  3.70 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4109.23 seconds
wall clock time: 70 minutes 57.87 seconds (4257.87 seconds total)