Starting phenix.real_space_refine
on Wed Mar 12 13:53:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsp_60423/03_2025/8zsp_60423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsp_60423/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zsp_60423/03_2025/8zsp_60423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsp_60423/03_2025/8zsp_60423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsp_60423/03_2025/8zsp_60423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsp_60423/03_2025/8zsp_60423.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 2, 'PHE:plan': 2, 'HIS:plan': 3, 'ARG:plan': 2, 'GLU:plan': 2}
          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: 5.19, per 1000 atoms: 0.64
  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: 2.06
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.84
  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: 2.28

  Time building geometry restraints manager: 2.35 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.410
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.940
-------------------------------------------------------------------------------
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   8251  Z= 0.541
  Angle     :  0.718  13.844  11192  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (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
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.015   0.001   PHE B 234 
 TYR   0.011   0.001   TYR B 105 
 ARG   0.003   0.000   ARG B  49 

*********************** 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  : 0.944 
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: 0.7797 (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: 0.6849 (m)
REVERT: N   60 TYR cc_start: 0.8396 (m-80) cc_final: 0.7895 (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: 0.2478
  time to fit residues: 75.8412
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  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 155 ASN
B 176 GLN
** B 259 GLN ** 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 = 0.3811 r_free = 0.3811 target = 0.137845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.120386 restraints weight = 11674.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.40
r_work: 0.3466 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8251  Z= 0.239
  Angle     :  0.559   7.696  11192  Z= 0.300
  Chirality :  0.044   0.149   1258
  Planarity :  0.004   0.042   1427
  Dihedral  :  6.514 138.672   1147
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 12.76 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1019
  helix:  1.71 (0.26), residues: 397
  sheet: -0.40 (0.36), residues: 190
  loop : -0.71 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 211 
 HIS   0.007   0.001   HIS R 113 
 PHE   0.016   0.002   PHE R 156 
 TYR   0.016   0.001   TYR A 115 
 ARG   0.006   0.000   ARG B  49 

*********************** 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
  245 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 235
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 SER cc_start: 0.8379 (p) cc_final: 0.8166 (m)
REVERT: A   71 GLU cc_start: 0.7356 (tp30) cc_final: 0.7062 (tp30)
REVERT: A  166 GLU cc_start: 0.8301 (mp0) cc_final: 0.7984 (mp0)
REVERT: A  177 THR cc_start: 0.8465 (m) cc_final: 0.8036 (p)
REVERT: B   10 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: B   68 ARG cc_start: 0.8104 (ttt180) cc_final: 0.7697 (ttt180)
REVERT: B   86 THR cc_start: 0.8334 (p) cc_final: 0.7805 (p)
REVERT: B   88 ASN cc_start: 0.8184 (m-40) cc_final: 0.7718 (m110)
REVERT: B  118 ASP cc_start: 0.7983 (p0) cc_final: 0.7765 (p0)
REVERT: B  163 ASP cc_start: 0.7413 (t0) cc_final: 0.7080 (t70)
REVERT: B  212 ASP cc_start: 0.7917 (t0) cc_final: 0.7520 (t0)
REVERT: B  241 PHE cc_start: 0.8460 (p90) cc_final: 0.8252 (p90)
REVERT: B  258 ASP cc_start: 0.8538 (t0) cc_final: 0.8087 (t0)
REVERT: B  271 CYS cc_start: 0.8109 (m) cc_final: 0.7749 (m)
REVERT: B  297 TRP cc_start: 0.8489 (m100) cc_final: 0.8278 (m100)
REVERT: G   21 MET cc_start: 0.6825 (mmp) cc_final: 0.6542 (mmp)
REVERT: N   60 TYR cc_start: 0.8501 (m-80) cc_final: 0.8170 (m-80)
REVERT: R   43 ILE cc_start: 0.7605 (mt) cc_final: 0.7323 (mt)
REVERT: R   51 PHE cc_start: 0.7526 (m-80) cc_final: 0.7319 (m-80)
REVERT: R   55 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.8028 (m90)
REVERT: R  273 MET cc_start: 0.7478 (mtm) cc_final: 0.7075 (mtm)
  outliers start: 10
  outliers final: 2
  residues processed: 237
  average time/residue: 0.2352
  time to fit residues: 72.1305
Evaluate side-chains
  226 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 223
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   55 HIS
Chi-restraints excluded: chain R residue  140 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    0.2980
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 88 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0470
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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**
** B 295 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 = 0.3823 r_free = 0.3823 target = 0.138779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121437 restraints weight = 11753.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.39
r_work: 0.3483 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8251  Z= 0.159
  Angle     :  0.506   8.019  11192  Z= 0.266
  Chirality :  0.042   0.144   1258
  Planarity :  0.004   0.044   1427
  Dihedral  :  5.767 119.977   1147
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 1019
  helix:  1.94 (0.26), residues: 405
  sheet: -0.31 (0.35), residues: 199
  loop : -0.57 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.019   0.001   PHE A 228 
 TYR   0.015   0.001   TYR A 115 
 ARG   0.007   0.000   ARG B  49 

*********************** 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
  248 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 235
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8443 (mp0) cc_final: 0.8067 (mp0)
REVERT: A   71 GLU cc_start: 0.7359 (tp30) cc_final: 0.7072 (tp30)
REVERT: A   74 PHE cc_start: 0.7856 (p90) cc_final: 0.7337 (p90)
REVERT: A  166 GLU cc_start: 0.8316 (mp0) cc_final: 0.8009 (mp0)
REVERT: A  177 THR cc_start: 0.8428 (m) cc_final: 0.8017 (p)
REVERT: B   10 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7229 (tm-30)
REVERT: B   86 THR cc_start: 0.8308 (p) cc_final: 0.7728 (p)
REVERT: B   88 ASN cc_start: 0.8095 (m-40) cc_final: 0.7612 (m110)
REVERT: B  118 ASP cc_start: 0.7987 (p0) cc_final: 0.7787 (p0)
REVERT: B  163 ASP cc_start: 0.7500 (t0) cc_final: 0.6882 (t0)
REVERT: B  212 ASP cc_start: 0.7926 (t0) cc_final: 0.7643 (t0)
REVERT: B  271 CYS cc_start: 0.7965 (m) cc_final: 0.7611 (m)
REVERT: B  297 TRP cc_start: 0.8436 (m100) cc_final: 0.8233 (m100)
REVERT: G   21 MET cc_start: 0.6777 (mmp) cc_final: 0.6508 (mmp)
REVERT: N   60 TYR cc_start: 0.8457 (m-80) cc_final: 0.8241 (m-80)
REVERT: R  135 MET cc_start: 0.7551 (mmm) cc_final: 0.7312 (mmm)
REVERT: R  143 MET cc_start: 0.8184 (mtt) cc_final: 0.7949 (mtt)
REVERT: R  273 MET cc_start: 0.7437 (mtm) cc_final: 0.7076 (mtm)
  outliers start: 13
  outliers final: 10
  residues processed: 237
  average time/residue: 0.2350
  time to fit residues: 72.6486
Evaluate side-chains
  235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
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  222 GLU
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  302 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 41 optimal weight:    0.0070
   chunk 70 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0040
   chunk 33 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7412

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

Flipped N/Q/H residues before XYZ refinement:
A 223 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
N  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.120527 restraints weight = 11791.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.36
r_work: 0.3475 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3310 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8251  Z= 0.207
  Angle     :  0.522  10.330  11192  Z= 0.272
  Chirality :  0.043   0.201   1258
  Planarity :  0.004   0.045   1427
  Dihedral  :  5.288  98.588   1147
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1019
  helix:  1.99 (0.26), residues: 401
  sheet: -0.36 (0.35), residues: 202
  loop : -0.49 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.028   0.002   PHE R 185 
 TYR   0.016   0.001   TYR A 115 
 ARG   0.008   0.000   ARG B  49 

*********************** 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
  249 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 233
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8540 (mp0) cc_final: 0.8171 (mp0)
REVERT: A   24 MET cc_start: 0.8191 (tmm) cc_final: 0.7802 (tmm)
REVERT: A   71 GLU cc_start: 0.7651 (tp30) cc_final: 0.7371 (tp30)
REVERT: A   74 PHE cc_start: 0.7959 (p90) cc_final: 0.7528 (p90)
REVERT: A  132 ARG cc_start: 0.7878 (ttt180) cc_final: 0.7639 (ttt180)
REVERT: A  166 GLU cc_start: 0.8475 (mp0) cc_final: 0.8168 (mp0)
REVERT: A  170 TYR cc_start: 0.8449 (t80) cc_final: 0.7756 (t80)
REVERT: A  177 THR cc_start: 0.8470 (m) cc_final: 0.8056 (p)
REVERT: B   10 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: B   45 MET cc_start: 0.8356 (mtt) cc_final: 0.8130 (mtp)
REVERT: B   86 THR cc_start: 0.8356 (p) cc_final: 0.7808 (p)
REVERT: B   88 ASN cc_start: 0.8156 (m-40) cc_final: 0.7706 (m-40)
REVERT: B  118 ASP cc_start: 0.8246 (p0) cc_final: 0.7981 (p0)
REVERT: B  137 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7949 (tpp80)
REVERT: B  163 ASP cc_start: 0.7723 (t0) cc_final: 0.7114 (t0)
REVERT: B  212 ASP cc_start: 0.8130 (t0) cc_final: 0.7810 (t0)
REVERT: B  251 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7747 (ttm170)
REVERT: B  258 ASP cc_start: 0.8665 (t0) cc_final: 0.8410 (t0)
REVERT: B  271 CYS cc_start: 0.8217 (m) cc_final: 0.7854 (m)
REVERT: G   21 MET cc_start: 0.6959 (mmp) cc_final: 0.6686 (mmp)
REVERT: N   60 TYR cc_start: 0.8615 (m-80) cc_final: 0.8411 (m-80)
REVERT: R  273 MET cc_start: 0.7755 (mtm) cc_final: 0.7426 (mtm)
  outliers start: 16
  outliers final: 13
  residues processed: 237
  average time/residue: 0.2205
  time to fit residues: 68.9498
Evaluate side-chains
  244 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 231
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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 R residue   71 LEU
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  302 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.137143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.119654 restraints weight = 11639.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 2.38
r_work: 0.3451 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8251  Z= 0.285
  Angle     :  0.560  10.776  11192  Z= 0.291
  Chirality :  0.044   0.226   1258
  Planarity :  0.004   0.045   1427
  Dihedral  :  5.070  83.510   1147
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.45 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.26), residues: 1019
  helix:  1.97 (0.26), residues: 395
  sheet: -0.30 (0.34), residues: 201
  loop : -0.55 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.024   0.002   PHE R 185 
 TYR   0.020   0.002   TYR A 115 
 ARG   0.009   0.000   ARG B  49 

*********************** 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: 19
    poor density    : 228
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8561 (mp0) cc_final: 0.8202 (mp0)
REVERT: A   24 MET cc_start: 0.8265 (tmm) cc_final: 0.7838 (tmm)
REVERT: A   71 GLU cc_start: 0.7748 (tp30) cc_final: 0.7474 (tp30)
REVERT: A   74 PHE cc_start: 0.7936 (p90) cc_final: 0.7584 (p90)
REVERT: A  132 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7615 (ttt180)
REVERT: A  166 GLU cc_start: 0.8502 (mp0) cc_final: 0.8168 (mp0)
REVERT: A  170 TYR cc_start: 0.8519 (t80) cc_final: 0.7790 (t80)
REVERT: A  177 THR cc_start: 0.8493 (m) cc_final: 0.8077 (p)
REVERT: B   54 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.8097 (m-70)
REVERT: B   86 THR cc_start: 0.8321 (p) cc_final: 0.7773 (p)
REVERT: B   88 ASN cc_start: 0.8164 (m-40) cc_final: 0.7699 (m-40)
REVERT: B  118 ASP cc_start: 0.8269 (p0) cc_final: 0.7995 (p0)
REVERT: B  163 ASP cc_start: 0.7733 (t0) cc_final: 0.7114 (t0)
REVERT: B  212 ASP cc_start: 0.8136 (t0) cc_final: 0.7812 (t0)
REVERT: B  258 ASP cc_start: 0.8655 (t0) cc_final: 0.8336 (t0)
REVERT: B  271 CYS cc_start: 0.8320 (m) cc_final: 0.7966 (m)
REVERT: G   21 MET cc_start: 0.7009 (mmp) cc_final: 0.6712 (mmp)
REVERT: N   60 TYR cc_start: 0.8596 (m-80) cc_final: 0.8335 (m-80)
REVERT: R  100 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7047 (p)
REVERT: R  273 MET cc_start: 0.7774 (mtm) cc_final: 0.7473 (mtm)
  outliers start: 19
  outliers final: 14
  residues processed: 233
  average time/residue: 0.2282
  time to fit residues: 69.3758
Evaluate side-chains
  242 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 226
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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  187 THR
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain B residue   54 HIS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   80 SER
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  271 THR
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 32 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.138296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120903 restraints weight = 11614.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.36
r_work: 0.3476 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8251  Z= 0.200
  Angle     :  0.554  14.514  11192  Z= 0.280
  Chirality :  0.044   0.292   1258
  Planarity :  0.004   0.047   1427
  Dihedral  :  4.824  75.850   1147
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.26 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1019
  helix:  1.93 (0.26), residues: 400
  sheet: -0.35 (0.35), residues: 201
  loop : -0.46 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.011   0.001   HIS B  54 
 PHE   0.025   0.002   PHE R 185 
 TYR   0.020   0.001   TYR A 115 
 ARG   0.009   0.000   ARG B  49 

*********************** 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
  235 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8540 (mp0) cc_final: 0.8207 (mp0)
REVERT: A   71 GLU cc_start: 0.7734 (tp30) cc_final: 0.7474 (tp30)
REVERT: A   74 PHE cc_start: 0.7904 (p90) cc_final: 0.7513 (p90)
REVERT: A   77 ASP cc_start: 0.8002 (m-30) cc_final: 0.7717 (m-30)
REVERT: A  132 ARG cc_start: 0.7828 (ttt180) cc_final: 0.7556 (ttt180)
REVERT: A  166 GLU cc_start: 0.8466 (mp0) cc_final: 0.8138 (mp0)
REVERT: A  170 TYR cc_start: 0.8510 (t80) cc_final: 0.7739 (t80)
REVERT: A  210 TYR cc_start: 0.7957 (m-80) cc_final: 0.7717 (m-80)
REVERT: B   45 MET cc_start: 0.8441 (mtt) cc_final: 0.8227 (mtp)
REVERT: B   86 THR cc_start: 0.8328 (p) cc_final: 0.7737 (p)
REVERT: B   88 ASN cc_start: 0.8149 (m-40) cc_final: 0.7691 (m110)
REVERT: B  118 ASP cc_start: 0.8238 (p0) cc_final: 0.7962 (p0)
REVERT: B  137 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7745 (tpp80)
REVERT: B  163 ASP cc_start: 0.7708 (t0) cc_final: 0.7086 (t0)
REVERT: B  212 ASP cc_start: 0.8080 (t0) cc_final: 0.7773 (t0)
REVERT: B  227 SER cc_start: 0.8229 (t) cc_final: 0.7885 (p)
REVERT: B  251 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7685 (ttm170)
REVERT: B  258 ASP cc_start: 0.8648 (t0) cc_final: 0.8313 (t0)
REVERT: B  271 CYS cc_start: 0.8282 (m) cc_final: 0.7894 (m)
REVERT: G   21 MET cc_start: 0.6992 (mmp) cc_final: 0.6709 (mmp)
REVERT: R  273 MET cc_start: 0.7791 (mtm) cc_final: 0.7490 (mtm)
  outliers start: 15
  outliers final: 9
  residues processed: 225
  average time/residue: 0.2422
  time to fit residues: 70.2512
Evaluate side-chains
  222 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 213
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  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 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 35 optimal weight:    0.0270
   chunk 94 optimal weight:    0.4980
   chunk 64 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.1242

-------------------------------------------------------------------------------
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 230 ASN
** B 259 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.136204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119346 restraints weight = 11713.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.32
r_work: 0.3446 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8251  Z= 0.274
  Angle     :  0.588  18.723  11192  Z= 0.298
  Chirality :  0.045   0.351   1258
  Planarity :  0.004   0.046   1427
  Dihedral  :  4.801  69.006   1147
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.84 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1019
  helix:  1.89 (0.26), residues: 394
  sheet: -0.42 (0.34), residues: 201
  loop : -0.46 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.023   0.002   PHE B 241 
 TYR   0.026   0.002   TYR N 115 
 ARG   0.010   0.000   ARG B  49 

*********************** 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
  240 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 225
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8549 (mp0) cc_final: 0.8222 (mp0)
REVERT: A   71 GLU cc_start: 0.7754 (tp30) cc_final: 0.7521 (tp30)
REVERT: A   74 PHE cc_start: 0.7902 (p90) cc_final: 0.7480 (p90)
REVERT: A   77 ASP cc_start: 0.8008 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  132 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7611 (ttt180)
REVERT: A  166 GLU cc_start: 0.8461 (mp0) cc_final: 0.8149 (mp0)
REVERT: A  170 TYR cc_start: 0.8519 (t80) cc_final: 0.7735 (t80)
REVERT: A  210 TYR cc_start: 0.7936 (m-80) cc_final: 0.7731 (m-80)
REVERT: A  228 PHE cc_start: 0.8578 (t80) cc_final: 0.8298 (t80)
REVERT: B   45 MET cc_start: 0.8468 (mtt) cc_final: 0.8214 (mtp)
REVERT: B   49 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8019 (mmt-90)
REVERT: B   83 ASP cc_start: 0.8519 (t0) cc_final: 0.8186 (t70)
REVERT: B   86 THR cc_start: 0.8320 (p) cc_final: 0.7605 (p)
REVERT: B   88 ASN cc_start: 0.8173 (m-40) cc_final: 0.7702 (m-40)
REVERT: B  118 ASP cc_start: 0.8172 (p0) cc_final: 0.7899 (p0)
REVERT: B  137 ARG cc_start: 0.8299 (tpp80) cc_final: 0.7793 (tpp80)
REVERT: B  163 ASP cc_start: 0.7756 (t0) cc_final: 0.7160 (t0)
REVERT: B  212 ASP cc_start: 0.8110 (t0) cc_final: 0.7802 (t0)
REVERT: B  227 SER cc_start: 0.8320 (t) cc_final: 0.7949 (p)
REVERT: B  251 ARG cc_start: 0.7897 (mtt90) cc_final: 0.7586 (ttm170)
REVERT: B  258 ASP cc_start: 0.8683 (t0) cc_final: 0.8352 (t0)
REVERT: B  265 SER cc_start: 0.8809 (t) cc_final: 0.8513 (p)
REVERT: B  271 CYS cc_start: 0.8294 (m) cc_final: 0.7915 (m)
REVERT: G   21 MET cc_start: 0.6970 (mmp) cc_final: 0.6681 (mmp)
REVERT: R  273 MET cc_start: 0.7846 (mtm) cc_final: 0.7575 (mtm)
  outliers start: 15
  outliers final: 10
  residues processed: 231
  average time/residue: 0.2251
  time to fit residues: 67.9316
Evaluate side-chains
  230 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 220
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
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  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 N residue   21 SER
Chi-restraints excluded: chain R residue  119 ILE
Chi-restraints excluded: chain R residue  223 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0060
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 237 ASN
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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.138046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121559 restraints weight = 11900.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.28
r_work: 0.3474 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8251  Z= 0.189
  Angle     :  0.574  15.076  11192  Z= 0.286
  Chirality :  0.044   0.269   1258
  Planarity :  0.004   0.038   1427
  Dihedral  :  4.648  66.056   1147
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 21.00 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.26), residues: 1019
  helix:  2.01 (0.26), residues: 394
  sheet: -0.47 (0.34), residues: 201
  loop : -0.45 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 211 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.023   0.001   PHE B 241 
 TYR   0.025   0.001   TYR N 115 
 ARG   0.008   0.000   ARG B  49 

*********************** 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
  236 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 221
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8534 (mp0) cc_final: 0.8257 (mp0)
REVERT: A   71 GLU cc_start: 0.7729 (tp30) cc_final: 0.7468 (tp30)
REVERT: A   74 PHE cc_start: 0.7861 (p90) cc_final: 0.7431 (p90)
REVERT: A   77 ASP cc_start: 0.7957 (m-30) cc_final: 0.7634 (m-30)
REVERT: A   83 MET cc_start: 0.8577 (mtp) cc_final: 0.8268 (mtm)
REVERT: A  132 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7530 (ttt180)
REVERT: A  166 GLU cc_start: 0.8422 (mp0) cc_final: 0.8128 (mp0)
REVERT: A  228 PHE cc_start: 0.8527 (t80) cc_final: 0.8279 (t80)
REVERT: B   45 MET cc_start: 0.8480 (mtt) cc_final: 0.8220 (mtp)
REVERT: B   49 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.8084 (mmt-90)
REVERT: B   86 THR cc_start: 0.8382 (p) cc_final: 0.7841 (p)
REVERT: B   88 ASN cc_start: 0.8141 (m-40) cc_final: 0.7683 (m-40)
REVERT: B  118 ASP cc_start: 0.8130 (p0) cc_final: 0.7867 (p0)
REVERT: B  137 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7763 (tpp80)
REVERT: B  163 ASP cc_start: 0.7686 (t0) cc_final: 0.7094 (t0)
REVERT: B  212 ASP cc_start: 0.8050 (t0) cc_final: 0.7771 (t0)
REVERT: B  227 SER cc_start: 0.8267 (t) cc_final: 0.7903 (p)
REVERT: B  258 ASP cc_start: 0.8642 (t0) cc_final: 0.8320 (t0)
REVERT: B  265 SER cc_start: 0.8803 (t) cc_final: 0.8450 (p)
REVERT: B  271 CYS cc_start: 0.8265 (m) cc_final: 0.7906 (m)
REVERT: B  296 VAL cc_start: 0.8439 (t) cc_final: 0.8187 (m)
REVERT: G   21 MET cc_start: 0.6886 (mmp) cc_final: 0.6601 (mmp)
REVERT: N  112 SER cc_start: 0.8073 (m) cc_final: 0.7718 (m)
REVERT: R   43 ILE cc_start: 0.7756 (mt) cc_final: 0.7505 (mt)
REVERT: R  273 MET cc_start: 0.7752 (mtm) cc_final: 0.7492 (mtm)
  outliers start: 15
  outliers final: 10
  residues processed: 229
  average time/residue: 0.2182
  time to fit residues: 65.7415
Evaluate side-chains
  230 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 220
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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 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 36 optimal weight:    0.1980
   chunk 60 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.139750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.123309 restraints weight = 12037.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.32
r_work: 0.3493 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8251  Z= 0.157
  Angle     :  0.551  13.570  11192  Z= 0.278
  Chirality :  0.042   0.222   1258
  Planarity :  0.004   0.039   1427
  Dihedral  :  4.484  60.968   1147
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.81 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.26), residues: 1019
  helix:  2.09 (0.26), residues: 394
  sheet: -0.45 (0.35), residues: 201
  loop : -0.40 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 148 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.026   0.001   PHE B 241 
 TYR   0.021   0.001   TYR N 115 
 ARG   0.008   0.000   ARG A 194 

*********************** 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
  234 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 220
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8562 (mp0) cc_final: 0.8322 (mp0)
REVERT: A   77 ASP cc_start: 0.7947 (m-30) cc_final: 0.7682 (m-30)
REVERT: A   83 MET cc_start: 0.8548 (mtp) cc_final: 0.8288 (mtm)
REVERT: A  132 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7469 (ttt180)
REVERT: A  166 GLU cc_start: 0.8427 (mp0) cc_final: 0.8136 (mp0)
REVERT: A  225 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7695 (tpt90)
REVERT: B   49 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.8077 (mmt-90)
REVERT: B   86 THR cc_start: 0.8376 (p) cc_final: 0.7820 (p)
REVERT: B   88 ASN cc_start: 0.8106 (m-40) cc_final: 0.7664 (m110)
REVERT: B  102 THR cc_start: 0.8420 (t) cc_final: 0.8213 (t)
REVERT: B  118 ASP cc_start: 0.8120 (p0) cc_final: 0.7837 (p0)
REVERT: B  137 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7712 (tpp80)
REVERT: B  163 ASP cc_start: 0.7684 (t0) cc_final: 0.7102 (t0)
REVERT: B  212 ASP cc_start: 0.8033 (t0) cc_final: 0.7755 (t0)
REVERT: B  227 SER cc_start: 0.8274 (t) cc_final: 0.7891 (p)
REVERT: B  258 ASP cc_start: 0.8603 (t0) cc_final: 0.8288 (t0)
REVERT: B  271 CYS cc_start: 0.8225 (m) cc_final: 0.7869 (m)
REVERT: B  296 VAL cc_start: 0.8421 (t) cc_final: 0.8174 (m)
REVERT: G   21 MET cc_start: 0.6895 (mmp) cc_final: 0.6603 (mmp)
REVERT: N  112 SER cc_start: 0.8064 (m) cc_final: 0.7720 (m)
REVERT: R   43 ILE cc_start: 0.7715 (mt) cc_final: 0.7462 (mt)
REVERT: R  273 MET cc_start: 0.7756 (mtm) cc_final: 0.7479 (mtm)
  outliers start: 14
  outliers final: 11
  residues processed: 224
  average time/residue: 0.2193
  time to fit residues: 64.8566
Evaluate side-chains
  225 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 214
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
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 N residue   21 SER
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 54 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 88 optimal weight:    8.9990
   chunk 73 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   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  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**

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 = 0.138902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122234 restraints weight = 11716.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.30
r_work: 0.3483 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8251  Z= 0.192
  Angle     :  0.579  14.224  11192  Z= 0.289
  Chirality :  0.044   0.243   1258
  Planarity :  0.004   0.038   1427
  Dihedral  :  4.421  54.553   1147
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.39 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1019
  helix:  2.07 (0.26), residues: 392
  sheet: -0.45 (0.35), residues: 201
  loop : -0.44 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 148 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.026   0.001   PHE B 241 
 TYR   0.022   0.001   TYR N 115 
 ARG   0.007   0.000   ARG A 194 

********************** 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: 14
    poor density    : 219
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.8573 (mp0) cc_final: 0.8322 (mp0)
REVERT: A   74 PHE cc_start: 0.7910 (p90) cc_final: 0.7570 (p90)
REVERT: A   77 ASP cc_start: 0.8004 (m-30) cc_final: 0.7630 (m-30)
REVERT: A  132 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7541 (ttt180)
REVERT: A  166 GLU cc_start: 0.8437 (mp0) cc_final: 0.8148 (mp0)
REVERT: A  225 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.8048 (tpp-160)
REVERT: B   45 MET cc_start: 0.8417 (mtt) cc_final: 0.8211 (mtp)
REVERT: B   49 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.8032 (mmt-90)
REVERT: B   83 ASP cc_start: 0.8453 (t0) cc_final: 0.8141 (t70)
REVERT: B   86 THR cc_start: 0.8343 (p) cc_final: 0.7654 (p)
REVERT: B   88 ASN cc_start: 0.8119 (m-40) cc_final: 0.7688 (m110)
REVERT: B  118 ASP cc_start: 0.8123 (p0) cc_final: 0.7867 (p0)
REVERT: B  137 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7855 (tpp80)
REVERT: B  163 ASP cc_start: 0.7684 (t0) cc_final: 0.7117 (t0)
REVERT: B  212 ASP cc_start: 0.8083 (t0) cc_final: 0.7792 (t0)
REVERT: B  227 SER cc_start: 0.8294 (t) cc_final: 0.7910 (p)
REVERT: B  258 ASP cc_start: 0.8620 (t0) cc_final: 0.8308 (t0)
REVERT: B  271 CYS cc_start: 0.8245 (m) cc_final: 0.7904 (m)
REVERT: B  296 VAL cc_start: 0.8423 (t) cc_final: 0.8152 (m)
REVERT: G   21 MET cc_start: 0.6945 (mmp) cc_final: 0.6647 (mmp)
REVERT: N  112 SER cc_start: 0.8099 (m) cc_final: 0.7757 (m)
REVERT: R   43 ILE cc_start: 0.7712 (mt) cc_final: 0.7450 (mt)
REVERT: R   72 LEU cc_start: 0.7129 (tt) cc_final: 0.6898 (tt)
REVERT: R  273 MET cc_start: 0.7786 (mtm) cc_final: 0.7520 (mtm)
  outliers start: 14
  outliers final: 10
  residues processed: 224
  average time/residue: 0.2286
  time to fit residues: 67.2609
Evaluate side-chains
  226 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 216
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
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 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 65 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0570
   chunk 48 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 99 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 132 ASN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.139179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.122834 restraints weight = 11848.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.28
r_work: 0.3494 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8251  Z= 0.178
  Angle     :  0.563  12.903  11192  Z= 0.284
  Chirality :  0.043   0.232   1258
  Planarity :  0.004   0.037   1427
  Dihedral  :  4.350  50.033   1147
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.85 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1019
  helix:  2.09 (0.26), residues: 395
  sheet: -0.54 (0.35), residues: 205
  loop : -0.49 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 148 
 HIS   0.005   0.001   HIS R 113 
 PHE   0.027   0.001   PHE B 241 
 TYR   0.021   0.001   TYR N 115 
 ARG   0.007   0.000   ARG A 194 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4393.71 seconds
wall clock time: 75 minutes 56.44 seconds (4556.44 seconds total)