Starting phenix.real_space_refine
on Wed Sep 17 10:07:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsp_60423/09_2025/8zsp_60423.map"
  }
  resolution = 3.14
  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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5129      2.51       5
     N    1390      2.21       5
     O    1498      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8076
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1874
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2597
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 434
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 434
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2180
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 59
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'7LD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.17, per 1000 atoms: 0.27
  Number of scatterers: 8076
  At special positions: 0
  Unit cell: (73.216, 98.176, 132.288, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1498      8.00
     N    1390      7.00
     C    5129      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.02

  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: 0.76
  Conformation dependent library (CDL) restraints added in 524.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1944

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      42.5% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.561A  pdb=" N   ALA A  38 " --> pdb=" O   GLU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.596A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
      removed outlier: 3.779A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 131
      removed outlier: 4.050A  pdb=" N   GLN A 119 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.239A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
      removed outlier: 3.515A  pdb=" N   ALA A 168 " --> pdb=" O   PRO A 165 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 165 through 168'
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 4.337A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 23 through 51
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 84
      removed outlier: 3.799A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 93 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 188 through 199
      removed outlier: 3.964A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 211
      removed outlier: 3.534A  pdb=" N   TYR R 210 " --> pdb=" O   MET R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 211 through 230
    Processing helix  chain 'R' and resid 248 through 274
      removed outlier: 3.880A  pdb=" N   PHE R 260 " --> pdb=" O   VAL R 256 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU R 261 " --> pdb=" O   MET R 257 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.678A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 318
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 75
      removed outlier: 10.034A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.802A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.698A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.692A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.890A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.812A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.707A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.979A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 5.813A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.435A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1209 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: 1.58

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1321
        1.31 -     1.44: 2298
        1.44 -     1.56: 4544
        1.56 -     1.69: 4
        1.69 -     1.81: 84
  Bond restraints: 8251
  Sorted by residual:
  bond pdb=" C12 7LD R 401 "
       pdb=" N2  7LD R 401 "
    ideal  model  delta    sigma   weight residual
    1.450  1.241  0.209 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" C13 7LD R 401 "
       pdb=" N2  7LD R 401 "
    ideal  model  delta    sigma   weight residual
    1.451  1.257  0.194 2.00e-02 2.50e+03 9.39e+01
  bond pdb=" C10 7LD R 401 "
       pdb=" C9  7LD R 401 "
    ideal  model  delta    sigma   weight residual
    1.333  1.509 -0.176 2.00e-02 2.50e+03 7.77e+01
  bond pdb=" C1  7LD R 401 "
       pdb=" C4  7LD R 401 "
    ideal  model  delta    sigma   weight residual
    1.395  1.568 -0.173 2.00e-02 2.50e+03 7.46e+01
  bond pdb=" C10 7LD R 401 "
       pdb=" C14 7LD R 401 "
    ideal  model  delta    sigma   weight residual
    1.501  1.333  0.168 2.00e-02 2.50e+03 7.09e+01
  ... (remaining 8246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 11048
        2.77 -     5.54: 135
        5.54 -     8.31: 6
        8.31 -    11.08: 2
       11.08 -    13.84: 1
  Bond angle restraints: 11192
  Sorted by residual:
  angle pdb=" N   ASP B 163 "
        pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     112.59   98.75   13.84 1.22e+00 6.72e-01 1.29e+02
  angle pdb=" C   MET R 158 "
        pdb=" N   ILE R 159 "
        pdb=" CA  ILE R 159 "
      ideal   model   delta    sigma   weight residual
     122.35  113.70    8.65 1.18e+00 7.18e-01 5.37e+01
  angle pdb=" N   ASP B 170 "
        pdb=" CA  ASP B 170 "
        pdb=" C   ASP B 170 "
      ideal   model   delta    sigma   weight residual
     109.07   99.73    9.34 1.61e+00 3.86e-01 3.37e+01
  angle pdb=" N   PHE R 156 "
        pdb=" CA  PHE R 156 "
        pdb=" C   PHE R 156 "
      ideal   model   delta    sigma   weight residual
     113.01  107.55    5.46 1.20e+00 6.94e-01 2.07e+01
  angle pdb=" N   LYS R 174 "
        pdb=" CA  LYS R 174 "
        pdb=" C   LYS R 174 "
      ideal   model   delta    sigma   weight residual
     111.28  106.50    4.78 1.09e+00 8.42e-01 1.92e+01
  ... (remaining 11187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.11: 4758
       31.11 -    62.22: 134
       62.22 -    93.32: 14
       93.32 -   124.43: 0
      124.43 -   155.54: 1
  Dihedral angle restraints: 4907
    sinusoidal: 1900
      harmonic: 3007
  Sorted by residual:
  dihedral pdb=" C16 7LD R 401 "
           pdb=" C17 7LD R 401 "
           pdb=" N3  7LD R 401 "
           pdb=" C18 7LD R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.75 -112.71 -155.54     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" N   ASP B 163 "
           pdb=" C   ASP B 163 "
           pdb=" CA  ASP B 163 "
           pdb=" CB  ASP B 163 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.75   10.05     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" CA  ASN B 237 "
           pdb=" C   ASN B 237 "
           pdb=" N   GLY B 238 "
           pdb=" CA  GLY B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.08  -18.92     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 983
       0.055 -    0.109: 217
       0.109 -    0.164: 51
       0.164 -    0.218: 5
       0.218 -    0.273: 2
  Chirality restraints: 1258
  Sorted by residual:
  chirality pdb=" CA  ASP B 163 "
            pdb=" N   ASP B 163 "
            pdb=" C   ASP B 163 "
            pdb=" CB  ASP B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  ILE R 171 "
            pdb=" N   ILE R 171 "
            pdb=" C   ILE R 171 "
            pdb=" CB  ILE R 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL R 184 "
            pdb=" CA  VAL R 184 "
            pdb=" CG1 VAL R 184 "
            pdb=" CG2 VAL R 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.21e-01
  ... (remaining 1255 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 152 "    0.011 2.00e-02 2.50e+03   2.29e-02 5.26e+00
        pdb=" C   ALA R 152 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ALA R 152 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL R 153 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO B 236 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 130 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   ARG R 130 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG R 130 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR R 131 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1719
        2.78 -     3.31: 8034
        3.31 -     3.84: 13848
        3.84 -     4.37: 16597
        4.37 -     4.90: 28528
  Nonbonded interactions: 68726
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 295 "
            pdb=" OG1 THR R 298 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR R  56 "
            pdb=" OD1 ASN R  59 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   CYS B 148 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.283 3.040
  ... (remaining 68721 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:             1.680
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.550
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
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      :  0.008   0.209   8254  Z= 0.444
  Angle     :  0.719  13.844  11198  Z= 0.459
  Chirality :  0.049   0.273   1258
  Planarity :  0.004   0.049   1427
  Dihedral  : 14.307 155.536   2954
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.16 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.27), residues: 1019
  helix:  1.53 (0.27), residues: 398
  sheet: -0.58 (0.38), residues: 187
  loop : -0.75 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.011   0.001   TYR B 105 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 ( 8251)
  covalent geometry    : angle       0.71786 (11192)
  SS BOND              : bond        0.00717 (    3)
  SS BOND              : angle       1.51228 (    6)
  hydrogen bonds       : bond        0.16665 (  418)
  hydrogen bonds       : angle       7.26698 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 GLU cc_start: 0.6839 (tp30) cc_final: 0.6610 (tp30)
REVERT: A  166 GLU cc_start: 0.8085 (mp0) cc_final: 0.7798 (mp0)
REVERT: B   10 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: B   86 THR cc_start: 0.8337 (p) cc_final: 0.7740 (p)
REVERT: B   88 ASN cc_start: 0.7917 (m-40) cc_final: 0.7558 (m110)
REVERT: B  118 ASP cc_start: 0.7322 (p0) cc_final: 0.7108 (p0)
REVERT: B  163 ASP cc_start: 0.7550 (t0) cc_final: 0.7169 (t70)
REVERT: B  189 SER cc_start: 0.8222 (t) cc_final: 0.7990 (p)
REVERT: B  271 CYS cc_start: 0.7082 (m) cc_final: 0.6848 (m)
REVERT: N   60 TYR cc_start: 0.8396 (m-80) cc_final: 0.7894 (m-80)
REVERT: R  145 PHE cc_start: 0.7755 (t80) cc_final: 0.7463 (t80)
REVERT: R  273 MET cc_start: 0.6544 (mtm) cc_final: 0.6212 (mtm)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1312
  time to fit residues: 39.9270
Evaluate side-chains
  211 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 146 GLN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 176 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  31 ASN
R  99 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.136711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119177 restraints weight = 11828.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.41
r_work: 0.3442 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8254  Z= 0.216
  Angle     :  0.590   8.070  11198  Z= 0.317
  Chirality :  0.045   0.148   1258
  Planarity :  0.004   0.043   1427
  Dihedral  :  6.623 139.225   1147
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.23 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.26), residues: 1019
  helix:  1.60 (0.26), residues: 397
  sheet: -0.45 (0.36), residues: 191
  loop : -0.72 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  49 
 TYR   0.018   0.002   TYR A 115 
 PHE   0.017   0.002   PHE R 156 
 TRP   0.023   0.002   TRP B 211 
 HIS   0.008   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 8251)
  covalent geometry    : angle       0.58931 (11192)
  SS BOND              : bond        0.00655 (    3)
  SS BOND              : angle       1.55129 (    6)
  hydrogen bonds       : bond        0.04662 (  418)
  hydrogen bonds       : angle       5.45969 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 245
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8407 (mp0) cc_final: 0.8005 (mp0)
REVERT: A   54 SER cc_start: 0.8392 (p) cc_final: 0.8179 (m)
REVERT: A   71 GLU cc_start: 0.7361 (tp30) cc_final: 0.7059 (tp30)
REVERT: A   74 PHE cc_start: 0.7899 (p90) cc_final: 0.7423 (p90)
REVERT: A  166 GLU cc_start: 0.8318 (mp0) cc_final: 0.7986 (mp0)
REVERT: A  177 THR cc_start: 0.8480 (m) cc_final: 0.8049 (p)
REVERT: B   10 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7248 (tm-30)
REVERT: B   86 THR cc_start: 0.8344 (p) cc_final: 0.7803 (p)
REVERT: B   88 ASN cc_start: 0.8185 (m-40) cc_final: 0.7716 (m110)
REVERT: B  118 ASP cc_start: 0.8046 (p0) cc_final: 0.7785 (p0)
REVERT: B  163 ASP cc_start: 0.7397 (t0) cc_final: 0.7052 (t70)
REVERT: B  212 ASP cc_start: 0.7939 (t0) cc_final: 0.7533 (t0)
REVERT: B  227 SER cc_start: 0.8030 (t) cc_final: 0.7721 (p)
REVERT: B  241 PHE cc_start: 0.8460 (p90) cc_final: 0.8257 (p90)
REVERT: B  258 ASP cc_start: 0.8556 (t0) cc_final: 0.8093 (t0)
REVERT: B  271 CYS cc_start: 0.8130 (m) cc_final: 0.7774 (m)
REVERT: B  297 TRP cc_start: 0.8488 (m100) cc_final: 0.8249 (m100)
REVERT: G   21 MET cc_start: 0.6864 (mmp) cc_final: 0.6574 (mmp)
REVERT: R   43 ILE cc_start: 0.7619 (mt) cc_final: 0.7387 (mt)
REVERT: R   55 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (m90)
REVERT: R  273 MET cc_start: 0.7489 (mtm) cc_final: 0.7115 (mtm)
  outliers start: 8
  outliers final: 1
  residues processed: 247
  average time/residue: 0.1209
  time to fit residues: 38.4277
Evaluate side-chains
  235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 233
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   55 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    0.4980
   chunk 89 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN
** R 296 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 = 0.3805 r_free = 0.3805 target = 0.137592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.120225 restraints weight = 11631.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.38
r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8254  Z= 0.143
  Angle     :  0.526   8.673  11198  Z= 0.278
  Chirality :  0.043   0.149   1258
  Planarity :  0.004   0.044   1427
  Dihedral  :  5.959 122.634   1147
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.85 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.26), residues: 1019
  helix:  1.87 (0.26), residues: 397
  sheet: -0.35 (0.35), residues: 199
  loop : -0.60 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  49 
 TYR   0.018   0.001   TYR A 115 
 PHE   0.016   0.002   PHE R 185 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8251)
  covalent geometry    : angle       0.52536 (11192)
  SS BOND              : bond        0.00478 (    3)
  SS BOND              : angle       1.20957 (    6)
  hydrogen bonds       : bond        0.04011 (  418)
  hydrogen bonds       : angle       5.14269 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 240
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8560 (mp0) cc_final: 0.8163 (mp0)
REVERT: A   24 MET cc_start: 0.8159 (tmm) cc_final: 0.7768 (tmm)
REVERT: A   54 SER cc_start: 0.8488 (p) cc_final: 0.8245 (m)
REVERT: A   71 GLU cc_start: 0.7638 (tp30) cc_final: 0.7259 (tp30)
REVERT: A   74 PHE cc_start: 0.7922 (p90) cc_final: 0.7451 (p90)
REVERT: A  132 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7609 (ttt180)
REVERT: A  166 GLU cc_start: 0.8483 (mp0) cc_final: 0.8132 (mp0)
REVERT: A  177 THR cc_start: 0.8498 (m) cc_final: 0.8074 (p)
REVERT: B   10 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7374 (tm-30)
REVERT: B   86 THR cc_start: 0.8380 (p) cc_final: 0.7870 (p)
REVERT: B   88 ASN cc_start: 0.8159 (m-40) cc_final: 0.7704 (m110)
REVERT: B  118 ASP cc_start: 0.8262 (p0) cc_final: 0.7986 (p0)
REVERT: B  163 ASP cc_start: 0.7700 (t0) cc_final: 0.7082 (t0)
REVERT: B  212 ASP cc_start: 0.8127 (t0) cc_final: 0.7827 (t0)
REVERT: B  227 SER cc_start: 0.8177 (t) cc_final: 0.7847 (p)
REVERT: B  271 CYS cc_start: 0.8283 (m) cc_final: 0.7942 (m)
REVERT: B  304 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8271 (ttm110)
REVERT: G   21 MET cc_start: 0.7022 (mmp) cc_final: 0.6749 (mmp)
REVERT: R   51 PHE cc_start: 0.7577 (m-80) cc_final: 0.7370 (m-80)
REVERT: R  273 MET cc_start: 0.7731 (mtm) cc_final: 0.7399 (mtm)
  outliers start: 16
  outliers final: 10
  residues processed: 242
  average time/residue: 0.1090
  time to fit residues: 34.6644
Evaluate side-chains
  246 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 236
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  140 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain R residue  302 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118136 restraints weight = 11875.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.40
r_work: 0.3425 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8254  Z= 0.244
  Angle     :  0.583  10.270  11198  Z= 0.307
  Chirality :  0.045   0.221   1258
  Planarity :  0.004   0.045   1427
  Dihedral  :  5.709 104.239   1147
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.17 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.26), residues: 1019
  helix:  1.81 (0.26), residues: 390
  sheet: -0.42 (0.35), residues: 202
  loop : -0.65 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  49 
 TYR   0.019   0.002   TYR A 115 
 PHE   0.025   0.002   PHE R 185 
 TRP   0.022   0.002   TRP R 148 
 HIS   0.006   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 8251)
  covalent geometry    : angle       0.58235 (11192)
  SS BOND              : bond        0.00496 (    3)
  SS BOND              : angle       1.12142 (    6)
  hydrogen bonds       : bond        0.04460 (  418)
  hydrogen bonds       : angle       5.23871 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 247
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8560 (mp0) cc_final: 0.8158 (mp0)
REVERT: A   24 MET cc_start: 0.8220 (tmm) cc_final: 0.7794 (tmm)
REVERT: A   71 GLU cc_start: 0.7699 (tp30) cc_final: 0.7396 (tp30)
REVERT: A   74 PHE cc_start: 0.7940 (p90) cc_final: 0.7571 (p90)
REVERT: A  132 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7703 (ttt180)
REVERT: A  161 GLU cc_start: 0.7127 (pm20) cc_final: 0.6783 (pm20)
REVERT: A  166 GLU cc_start: 0.8500 (mp0) cc_final: 0.8146 (mp0)
REVERT: A  177 THR cc_start: 0.8523 (m) cc_final: 0.8086 (p)
REVERT: B   86 THR cc_start: 0.8322 (p) cc_final: 0.7787 (p)
REVERT: B   88 ASN cc_start: 0.8184 (m-40) cc_final: 0.7678 (m-40)
REVERT: B  118 ASP cc_start: 0.8278 (p0) cc_final: 0.8016 (p0)
REVERT: B  163 ASP cc_start: 0.7729 (t0) cc_final: 0.7105 (t0)
REVERT: B  212 ASP cc_start: 0.8171 (t0) cc_final: 0.7850 (t0)
REVERT: B  258 ASP cc_start: 0.8713 (t0) cc_final: 0.8482 (t0)
REVERT: B  271 CYS cc_start: 0.8337 (m) cc_final: 0.8052 (m)
REVERT: G   21 MET cc_start: 0.7001 (mmp) cc_final: 0.6726 (mmp)
REVERT: R   77 MET cc_start: 0.8361 (mtt) cc_final: 0.8127 (mtt)
REVERT: R  273 MET cc_start: 0.7825 (mtm) cc_final: 0.7569 (mtm)
  outliers start: 18
  outliers final: 11
  residues processed: 249
  average time/residue: 0.1138
  time to fit residues: 36.7227
Evaluate side-chains
  252 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 241
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    0.0370
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 35 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.2262

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.136568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.119232 restraints weight = 11732.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.36
r_work: 0.3445 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8254  Z= 0.205
  Angle     :  0.579  10.330  11198  Z= 0.300
  Chirality :  0.045   0.220   1258
  Planarity :  0.004   0.046   1427
  Dihedral  :  5.326  89.366   1147
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 18.79 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.26), residues: 1019
  helix:  1.86 (0.26), residues: 390
  sheet: -0.43 (0.35), residues: 200
  loop : -0.63 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  49 
 TYR   0.029   0.002   TYR N 115 
 PHE   0.029   0.002   PHE R 185 
 TRP   0.019   0.002   TRP B 211 
 HIS   0.004   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 8251)
  covalent geometry    : angle       0.57855 (11192)
  SS BOND              : bond        0.00435 (    3)
  SS BOND              : angle       0.84956 (    6)
  hydrogen bonds       : bond        0.04170 (  418)
  hydrogen bonds       : angle       5.14539 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 235
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8566 (mp0) cc_final: 0.8176 (mp0)
REVERT: A   24 MET cc_start: 0.8215 (tmm) cc_final: 0.7776 (tmm)
REVERT: A   71 GLU cc_start: 0.7713 (tp30) cc_final: 0.7433 (tp30)
REVERT: A   74 PHE cc_start: 0.7899 (p90) cc_final: 0.7546 (p90)
REVERT: A  132 ARG cc_start: 0.7861 (ttt180) cc_final: 0.7603 (ttt180)
REVERT: A  161 GLU cc_start: 0.7137 (pm20) cc_final: 0.6812 (pm20)
REVERT: A  166 GLU cc_start: 0.8449 (mp0) cc_final: 0.8102 (mp0)
REVERT: A  177 THR cc_start: 0.8527 (m) cc_final: 0.8077 (p)
REVERT: B   86 THR cc_start: 0.8267 (p) cc_final: 0.7729 (p)
REVERT: B   88 ASN cc_start: 0.8177 (m-40) cc_final: 0.7658 (m-40)
REVERT: B  118 ASP cc_start: 0.8269 (p0) cc_final: 0.7985 (p0)
REVERT: B  163 ASP cc_start: 0.7716 (t0) cc_final: 0.7088 (t0)
REVERT: B  212 ASP cc_start: 0.8087 (t0) cc_final: 0.7790 (t0)
REVERT: B  227 SER cc_start: 0.8339 (t) cc_final: 0.7972 (p)
REVERT: B  258 ASP cc_start: 0.8671 (t0) cc_final: 0.8391 (t0)
REVERT: B  265 SER cc_start: 0.8818 (t) cc_final: 0.8465 (p)
REVERT: B  271 CYS cc_start: 0.8365 (m) cc_final: 0.8007 (m)
REVERT: G   21 MET cc_start: 0.6995 (mmp) cc_final: 0.6726 (mmp)
REVERT: N  112 SER cc_start: 0.8111 (m) cc_final: 0.7763 (m)
REVERT: N  115 TYR cc_start: 0.8433 (t80) cc_final: 0.8190 (t80)
REVERT: R  273 MET cc_start: 0.7833 (mtm) cc_final: 0.7562 (mtm)
  outliers start: 12
  outliers final: 10
  residues processed: 237
  average time/residue: 0.1088
  time to fit residues: 34.2281
Evaluate side-chains
  239 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 229
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 33 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
** R  55 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.137539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.120282 restraints weight = 11606.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.34
r_work: 0.3465 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8254  Z= 0.148
  Angle     :  0.543   8.946  11198  Z= 0.281
  Chirality :  0.043   0.235   1258
  Planarity :  0.004   0.048   1427
  Dihedral  :  4.907  75.204   1147
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.03 %
    Favored  : 78.89 %
  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 aren not related in a simple way.
  whole:  0.63 (0.26), residues: 1019
  helix:  2.01 (0.26), residues: 390
  sheet: -0.49 (0.34), residues: 201
  loop : -0.58 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  49 
 TYR   0.024   0.002   TYR N 115 
 PHE   0.026   0.002   PHE R 185 
 TRP   0.015   0.002   TRP B 211 
 HIS   0.004   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8251)
  covalent geometry    : angle       0.54256 (11192)
  SS BOND              : bond        0.00386 (    3)
  SS BOND              : angle       0.68803 (    6)
  hydrogen bonds       : bond        0.03869 (  418)
  hydrogen bonds       : angle       5.03303 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 229
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8542 (mp0) cc_final: 0.8169 (mp0)
REVERT: A   71 GLU cc_start: 0.7735 (tp30) cc_final: 0.7467 (tp30)
REVERT: A   74 PHE cc_start: 0.7862 (p90) cc_final: 0.7491 (p90)
REVERT: A  132 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7559 (ttt180)
REVERT: A  161 GLU cc_start: 0.7128 (pm20) cc_final: 0.6789 (pm20)
REVERT: A  166 GLU cc_start: 0.8474 (mp0) cc_final: 0.8131 (mp0)
REVERT: A  177 THR cc_start: 0.8502 (m) cc_final: 0.8056 (p)
REVERT: A  210 TYR cc_start: 0.7897 (m-80) cc_final: 0.7679 (m-80)
REVERT: B   49 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.8079 (mmt-90)
REVERT: B   86 THR cc_start: 0.8281 (p) cc_final: 0.7621 (p)
REVERT: B   88 ASN cc_start: 0.8166 (m-40) cc_final: 0.7657 (m-40)
REVERT: B  100 VAL cc_start: 0.8331 (m) cc_final: 0.8070 (p)
REVERT: B  118 ASP cc_start: 0.8230 (p0) cc_final: 0.7951 (p0)
REVERT: B  137 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8080 (tpp80)
REVERT: B  163 ASP cc_start: 0.7716 (t0) cc_final: 0.7068 (t0)
REVERT: B  212 ASP cc_start: 0.8072 (t0) cc_final: 0.7783 (t0)
REVERT: B  227 SER cc_start: 0.8303 (t) cc_final: 0.7945 (p)
REVERT: B  258 ASP cc_start: 0.8683 (t0) cc_final: 0.8377 (t0)
REVERT: B  271 CYS cc_start: 0.8324 (m) cc_final: 0.7935 (m)
REVERT: G   21 MET cc_start: 0.6991 (mmp) cc_final: 0.6703 (mmp)
REVERT: N  112 SER cc_start: 0.8125 (m) cc_final: 0.7782 (m)
REVERT: R  273 MET cc_start: 0.7785 (mtm) cc_final: 0.7522 (mtm)
  outliers start: 18
  outliers final: 11
  residues processed: 236
  average time/residue: 0.1052
  time to fit residues: 32.9295
Evaluate side-chains
  235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 224
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  297 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  55 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.137187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.120257 restraints weight = 11826.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.32
r_work: 0.3463 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8254  Z= 0.148
  Angle     :  0.547   8.696  11198  Z= 0.284
  Chirality :  0.043   0.242   1258
  Planarity :  0.004   0.046   1427
  Dihedral  :  4.642  61.752   1147
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.37 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1019
  helix:  2.03 (0.26), residues: 391
  sheet: -0.56 (0.34), residues: 201
  loop : -0.54 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  49 
 TYR   0.025   0.001   TYR N 115 
 PHE   0.022   0.001   PHE B 241 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8251)
  covalent geometry    : angle       0.54650 (11192)
  SS BOND              : bond        0.00349 (    3)
  SS BOND              : angle       0.58816 (    6)
  hydrogen bonds       : bond        0.03810 (  418)
  hydrogen bonds       : angle       5.00462 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8554 (mp0) cc_final: 0.8229 (mp0)
REVERT: A   71 GLU cc_start: 0.7740 (tp30) cc_final: 0.7488 (tp30)
REVERT: A   74 PHE cc_start: 0.7862 (p90) cc_final: 0.7503 (p90)
REVERT: A  132 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7581 (ttt180)
REVERT: A  161 GLU cc_start: 0.7093 (pm20) cc_final: 0.6794 (pm20)
REVERT: A  166 GLU cc_start: 0.8466 (mp0) cc_final: 0.8152 (mp0)
REVERT: A  177 THR cc_start: 0.8514 (m) cc_final: 0.8090 (p)
REVERT: B   49 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.8064 (mmt-90)
REVERT: B   86 THR cc_start: 0.8299 (p) cc_final: 0.7699 (p)
REVERT: B   88 ASN cc_start: 0.8147 (m-40) cc_final: 0.7648 (m-40)
REVERT: B  100 VAL cc_start: 0.8327 (m) cc_final: 0.8060 (p)
REVERT: B  118 ASP cc_start: 0.8134 (p0) cc_final: 0.7845 (p0)
REVERT: B  137 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8080 (tpp80)
REVERT: B  163 ASP cc_start: 0.7714 (t0) cc_final: 0.7098 (t0)
REVERT: B  212 ASP cc_start: 0.8066 (t0) cc_final: 0.7788 (t0)
REVERT: B  227 SER cc_start: 0.8289 (t) cc_final: 0.7967 (p)
REVERT: B  258 ASP cc_start: 0.8682 (t0) cc_final: 0.8365 (t0)
REVERT: B  271 CYS cc_start: 0.8277 (m) cc_final: 0.7912 (m)
REVERT: G   21 MET cc_start: 0.6960 (mmp) cc_final: 0.6672 (mmp)
REVERT: N  112 SER cc_start: 0.8094 (m) cc_final: 0.7744 (m)
REVERT: R  273 MET cc_start: 0.7811 (mtm) cc_final: 0.7549 (mtm)
  outliers start: 20
  outliers final: 14
  residues processed: 230
  average time/residue: 0.1072
  time to fit residues: 32.5961
Evaluate side-chains
  232 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 218
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  297 SER
Chi-restraints excluded: chain R residue  302 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0980
   chunk 82 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  55 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.138000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121558 restraints weight = 11815.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.29
r_work: 0.3478 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8254  Z= 0.134
  Angle     :  0.547   8.284  11198  Z= 0.283
  Chirality :  0.043   0.249   1258
  Planarity :  0.004   0.047   1427
  Dihedral  :  4.436  50.701   1147
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.77 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.27), residues: 1019
  helix:  2.08 (0.26), residues: 391
  sheet: -0.58 (0.34), residues: 201
  loop : -0.51 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  49 
 TYR   0.024   0.001   TYR N 115 
 PHE   0.024   0.001   PHE B 241 
 TRP   0.015   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8251)
  covalent geometry    : angle       0.54721 (11192)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       0.70310 (    6)
  hydrogen bonds       : bond        0.03719 (  418)
  hydrogen bonds       : angle       4.98063 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 224
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8574 (mp0) cc_final: 0.8254 (mp0)
REVERT: A   71 GLU cc_start: 0.7748 (tp30) cc_final: 0.7487 (tp30)
REVERT: A   74 PHE cc_start: 0.7857 (p90) cc_final: 0.7484 (p90)
REVERT: A  132 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7551 (ttt180)
REVERT: A  161 GLU cc_start: 0.7104 (pm20) cc_final: 0.6790 (pm20)
REVERT: A  166 GLU cc_start: 0.8434 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  177 THR cc_start: 0.8515 (m) cc_final: 0.8099 (p)
REVERT: B   49 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.8068 (mmt-90)
REVERT: B   86 THR cc_start: 0.8317 (p) cc_final: 0.7719 (p)
REVERT: B   88 ASN cc_start: 0.8142 (m-40) cc_final: 0.7656 (m110)
REVERT: B  100 VAL cc_start: 0.8296 (m) cc_final: 0.8024 (p)
REVERT: B  118 ASP cc_start: 0.8119 (p0) cc_final: 0.7845 (p0)
REVERT: B  137 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8069 (tpp80)
REVERT: B  163 ASP cc_start: 0.7711 (t0) cc_final: 0.7106 (t0)
REVERT: B  212 ASP cc_start: 0.8061 (t0) cc_final: 0.7777 (t0)
REVERT: B  227 SER cc_start: 0.8318 (t) cc_final: 0.7962 (p)
REVERT: B  258 ASP cc_start: 0.8642 (t0) cc_final: 0.8343 (t0)
REVERT: B  271 CYS cc_start: 0.8271 (m) cc_final: 0.7925 (m)
REVERT: B  278 PHE cc_start: 0.8717 (m-80) cc_final: 0.8495 (m-80)
REVERT: G   21 MET cc_start: 0.6948 (mmp) cc_final: 0.6666 (mmp)
REVERT: N  112 SER cc_start: 0.8102 (m) cc_final: 0.7782 (m)
REVERT: R   43 ILE cc_start: 0.7793 (mt) cc_final: 0.7533 (mt)
REVERT: R  273 MET cc_start: 0.7823 (mtm) cc_final: 0.7556 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 230
  average time/residue: 0.1098
  time to fit residues: 33.1619
Evaluate side-chains
  236 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 223
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  302 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0470
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.4292

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  55 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.139532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.123059 restraints weight = 11905.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.32
r_work: 0.3495 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8254  Z= 0.112
  Angle     :  0.531   8.069  11198  Z= 0.275
  Chirality :  0.042   0.239   1258
  Planarity :  0.004   0.047   1427
  Dihedral  :  4.128  36.127   1147
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.88 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.27), residues: 1019
  helix:  2.16 (0.26), residues: 392
  sheet: -0.54 (0.34), residues: 201
  loop : -0.47 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  49 
 TYR   0.021   0.001   TYR N 115 
 PHE   0.024   0.001   PHE B 241 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8251)
  covalent geometry    : angle       0.53122 (11192)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.76699 (    6)
  hydrogen bonds       : bond        0.03445 (  418)
  hydrogen bonds       : angle       4.91952 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 223
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8588 (mp0) cc_final: 0.8306 (mp0)
REVERT: A   71 GLU cc_start: 0.7730 (tp30) cc_final: 0.7482 (tp30)
REVERT: A   74 PHE cc_start: 0.7846 (p90) cc_final: 0.7504 (p90)
REVERT: A  132 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7525 (ttt180)
REVERT: A  166 GLU cc_start: 0.8427 (mp0) cc_final: 0.8121 (mp0)
REVERT: A  177 THR cc_start: 0.8506 (m) cc_final: 0.8114 (p)
REVERT: B   49 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.8088 (mmt-90)
REVERT: B   86 THR cc_start: 0.8257 (p) cc_final: 0.7696 (p)
REVERT: B   88 ASN cc_start: 0.8103 (m-40) cc_final: 0.7645 (m110)
REVERT: B  100 VAL cc_start: 0.8260 (m) cc_final: 0.7976 (p)
REVERT: B  118 ASP cc_start: 0.8141 (p0) cc_final: 0.7859 (p0)
REVERT: B  163 ASP cc_start: 0.7699 (t0) cc_final: 0.7097 (t0)
REVERT: B  212 ASP cc_start: 0.8047 (t0) cc_final: 0.7751 (t0)
REVERT: B  258 ASP cc_start: 0.8599 (t0) cc_final: 0.8329 (t0)
REVERT: B  271 CYS cc_start: 0.8249 (m) cc_final: 0.7909 (m)
REVERT: G   21 MET cc_start: 0.6930 (mmp) cc_final: 0.6633 (mmp)
REVERT: N  112 SER cc_start: 0.8117 (m) cc_final: 0.7800 (m)
REVERT: R   43 ILE cc_start: 0.7739 (mt) cc_final: 0.7469 (mt)
REVERT: R  273 MET cc_start: 0.7879 (mtm) cc_final: 0.7581 (mtm)
  outliers start: 17
  outliers final: 10
  residues processed: 228
  average time/residue: 0.1128
  time to fit residues: 33.6791
Evaluate side-chains
  229 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 219
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  302 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.138463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.122119 restraints weight = 11857.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.28
r_work: 0.3485 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8254  Z= 0.153
  Angle     :  0.568   9.677  11198  Z= 0.293
  Chirality :  0.044   0.238   1258
  Planarity :  0.004   0.039   1427
  Dihedral  :  4.164  38.918   1147
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 22.04 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 1019
  helix:  2.12 (0.26), residues: 391
  sheet: -0.66 (0.34), residues: 205
  loop : -0.55 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 194 
 TYR   0.023   0.001   TYR N 115 
 PHE   0.027   0.002   PHE B 241 
 TRP   0.018   0.002   TRP R 148 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8251)
  covalent geometry    : angle       0.56831 (11192)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.76106 (    6)
  hydrogen bonds       : bond        0.03736 (  418)
  hydrogen bonds       : angle       4.99949 ( 1209)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8565 (mp0) cc_final: 0.8288 (mp0)
REVERT: A   71 GLU cc_start: 0.7708 (tp30) cc_final: 0.7452 (tp30)
REVERT: A   74 PHE cc_start: 0.7870 (p90) cc_final: 0.7603 (p90)
REVERT: A  132 ARG cc_start: 0.7778 (ttt180) cc_final: 0.7533 (ttt180)
REVERT: A  166 GLU cc_start: 0.8395 (mp0) cc_final: 0.8118 (mp0)
REVERT: A  177 THR cc_start: 0.8511 (m) cc_final: 0.8115 (p)
REVERT: B   49 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8020 (mmt-90)
REVERT: B   86 THR cc_start: 0.8260 (p) cc_final: 0.7691 (p)
REVERT: B   88 ASN cc_start: 0.8119 (m-40) cc_final: 0.7648 (m110)
REVERT: B  100 VAL cc_start: 0.8323 (m) cc_final: 0.8053 (p)
REVERT: B  118 ASP cc_start: 0.8121 (p0) cc_final: 0.7849 (p0)
REVERT: B  163 ASP cc_start: 0.7675 (t0) cc_final: 0.7078 (t0)
REVERT: B  212 ASP cc_start: 0.8057 (t0) cc_final: 0.7771 (t0)
REVERT: B  227 SER cc_start: 0.8329 (m) cc_final: 0.8080 (p)
REVERT: B  258 ASP cc_start: 0.8665 (t0) cc_final: 0.8364 (t0)
REVERT: B  271 CYS cc_start: 0.8231 (m) cc_final: 0.7925 (m)
REVERT: G   21 MET cc_start: 0.6920 (mmp) cc_final: 0.6616 (mmp)
REVERT: N  112 SER cc_start: 0.8149 (m) cc_final: 0.7828 (m)
REVERT: R   43 ILE cc_start: 0.7745 (mt) cc_final: 0.7472 (mt)
REVERT: R  143 MET cc_start: 0.8355 (mtt) cc_final: 0.8082 (mtm)
REVERT: R  273 MET cc_start: 0.7847 (mtm) cc_final: 0.7565 (mtm)
  outliers start: 13
  outliers final: 12
  residues processed: 224
  average time/residue: 0.1070
  time to fit residues: 31.7598
Evaluate side-chains
  231 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 219
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   91 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  302 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   chunk 59 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.137805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.121645 restraints weight = 11844.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.26
r_work: 0.3479 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8254  Z= 0.152
  Angle     :  0.562   8.096  11198  Z= 0.292
  Chirality :  0.044   0.247   1258
  Planarity :  0.004   0.039   1427
  Dihedral  :  4.166  42.284   1147
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.04 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.27), residues: 1019
  helix:  1.95 (0.26), residues: 397
  sheet: -0.72 (0.34), residues: 205
  loop : -0.57 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 194 
 TYR   0.022   0.001   TYR N 115 
 PHE   0.028   0.002   PHE B 241 
 TRP   0.021   0.002   TRP R 148 
 HIS   0.005   0.001   HIS R 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8251)
  covalent geometry    : angle       0.56203 (11192)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       0.74539 (    6)
  hydrogen bonds       : bond        0.03780 (  418)
  hydrogen bonds       : angle       5.01089 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2372.54 seconds
wall clock time: 41 minutes 32.03 seconds (2492.03 seconds total)