Starting phenix.real_space_refine
on Wed Feb 12 20:31:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzq_27805/02_2025/8dzq_27805.cif"
  }
  resolution = 2.82
  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=   0.001 sd=   0.021
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      58      5.16       5
     C    5337      2.51       5
     N    1397      2.21       5
     O    1550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8342
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "C"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2484
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 79
    Chain: "D"
      Number of atoms: 292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 292
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "E"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1770
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1648
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 4, 'TRANS': 211}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 2117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2117
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 8, 'TRANS': 265}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'U99': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.54, per 1000 atoms: 0.66
  Number of scatterers: 8342
  At special positions: 0
  Unit cell: (90.64, 121.44, 127.6, 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      58     16.00
     O    1550      8.00
     N    1397      7.00
     C    5337      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 210 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.13
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2060

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      36.0% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'C' and resid 5 through 25
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 4.171A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN C 132 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 128 through 132'
    Processing helix  chain 'D' and resid 12 through 24
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.610A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.158A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 46 through 53
    Processing helix  chain 'B' and resid 212 through 217
      removed outlier: 3.538A  pdb=" N   CYS B 215 " --> pdb=" O   TRP B 212 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU B 217 " --> pdb=" O   HIS B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 232
      removed outlier: 4.534A  pdb=" N   ASP B 232 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 229 through 232'
    Processing helix  chain 'B' and resid 245 through 249
    Processing helix  chain 'B' and resid 251 through 256
    Processing helix  chain 'B' and resid 271 through 277
    Processing helix  chain 'B' and resid 296 through 310
      removed outlier: 4.342A  pdb=" N   ALA B 302 " --> pdb=" O   GLU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 351
      removed outlier: 4.165A  pdb=" N   VAL B 335 " --> pdb=" O   ASN B 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 87
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 92 through 110
    Processing helix  chain 'A' and resid 111 through 122
    Processing helix  chain 'A' and resid 127 through 162
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 171 through 197
      removed outlier: 3.869A  pdb=" N   VAL A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 235
    Processing helix  chain 'A' and resid 235 through 255
      removed outlier: 4.289A  pdb=" N   SER A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 299
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 306 through 331
      removed outlier: 3.720A  pdb=" N   TYR A 312 " --> pdb=" O   ALA A 308 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TYR A 313 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   PHE A 314 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      Proline residue:  A 327  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.786A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.763A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105
      removed outlier: 4.194A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.863A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 191 through 192
      removed outlier: 6.533A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.686A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.650A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.311A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.600A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192
      removed outlier: 3.662A  pdb=" N   ALA B 221 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ILE B 222 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   PHE B 268 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   PHE B 224 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ASN B 270 " --> pdb=" O   PHE B 224 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL B 226 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 198 through 200

    441 hydrogen bonds defined for protein.
    1233 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: 2.48

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1566
        1.33 -     1.45: 2172
        1.45 -     1.57: 4689
        1.57 -     1.70: 0
        1.70 -     1.82: 83
  Bond restraints: 8510
  Sorted by residual:
  bond pdb=" N   LEU E 166 "
       pdb=" CA  LEU E 166 "
    ideal  model  delta    sigma   weight residual
    1.455  1.477 -0.022 1.25e-02 6.40e+03 3.01e+00
  bond pdb=" CG1 ILE B 342 "
       pdb=" CD1 ILE B 342 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.60e+00
  bond pdb=" CA  ILE C  37 "
       pdb=" C   ILE C  37 "
    ideal  model  delta    sigma   weight residual
    1.518  1.533 -0.014 1.13e-02 7.83e+03 1.58e+00
  bond pdb=" CG  LEU B  38 "
       pdb=" CD2 LEU B  38 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CG1 ILE A 178 "
       pdb=" CD1 ILE A 178 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.53e+00
  ... (remaining 8505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11163
        1.80 -     3.60: 333
        3.60 -     5.40: 47
        5.40 -     7.21: 14
        7.21 -     9.01: 8
  Bond angle restraints: 11565
  Sorted by residual:
  angle pdb=" N   VAL B 202 "
        pdb=" CA  VAL B 202 "
        pdb=" C   VAL B 202 "
      ideal   model   delta    sigma   weight residual
     111.88  106.75    5.13 1.06e+00 8.90e-01 2.34e+01
  angle pdb=" C   ASN B 295 "
        pdb=" N   THR B 296 "
        pdb=" CA  THR B 296 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.17e+01
  angle pdb=" N   ARG C  68 "
        pdb=" CA  ARG C  68 "
        pdb=" C   ARG C  68 "
      ideal   model   delta    sigma   weight residual
     114.56  109.40    5.16 1.27e+00 6.20e-01 1.65e+01
  angle pdb=" C   ASN A 122 "
        pdb=" N   SER A 123 "
        pdb=" CA  SER A 123 "
      ideal   model   delta    sigma   weight residual
     121.54  114.59    6.95 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" N   ILE C  37 "
        pdb=" CA  ILE C  37 "
        pdb=" C   ILE C  37 "
      ideal   model   delta    sigma   weight residual
     112.98  108.49    4.49 1.25e+00 6.40e-01 1.29e+01
  ... (remaining 11560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 4573
       17.01 -    34.02: 405
       34.02 -    51.03: 60
       51.03 -    68.04: 9
       68.04 -    85.04: 7
  Dihedral angle restraints: 5054
    sinusoidal: 1868
      harmonic: 3186
  Sorted by residual:
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS A 210 "
           pdb=" CB  CYS A 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.52   79.52     1      1.00e+01 1.00e-02 7.85e+01
  dihedral pdb=" CA  LEU B 199 "
           pdb=" C   LEU B 199 "
           pdb=" N   PHE B 200 "
           pdb=" CA  PHE B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  LYS C  78 "
           pdb=" C   LYS C  78 "
           pdb=" N   LEU C  79 "
           pdb=" CA  LEU C  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.51   19.49     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5051 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1156
       0.068 -    0.136: 197
       0.136 -    0.203: 6
       0.203 -    0.271: 1
       0.271 -    0.339: 2
  Chirality restraints: 1362
  Sorted by residual:
  chirality pdb=" CG  LEU B 269 "
            pdb=" CB  LEU B 269 "
            pdb=" CD1 LEU B 269 "
            pdb=" CD2 LEU B 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C22 U99 A 401 "
            pdb=" C20 U99 A 401 "
            pdb=" C23 U99 A 401 "
            pdb=" C8  U99 A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.23   -1.93   -0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  VAL B 202 "
            pdb=" CA  VAL B 202 "
            pdb=" CG1 VAL B 202 "
            pdb=" CG2 VAL B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 1359 not shown)

  Planarity restraints: 1445
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 137 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   ARG C 137 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ARG C 137 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU C 138 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E 165 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   PHE E 165 "    0.041 2.00e-02 2.50e+03
        pdb=" O   PHE E 165 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU E 166 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 246 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.81e+00
        pdb=" C   ALA B 246 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ALA B 246 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 247 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1442 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1635
        2.78 -     3.31: 7688
        3.31 -     3.84: 13707
        3.84 -     4.37: 15878
        4.37 -     4.90: 28121
  Nonbonded interactions: 67029
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 245 "
            pdb=" OD1 ASP C 247 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   GLY E   8 "
            pdb=" OG1 THR E 115 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR C  86 "
            pdb=" OD1 ASN C  88 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OD2 ASP C 186 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   ALA C 231 "
            pdb=" OG1 THR C 243 "
     model   vdw
     2.309 3.040
  ... (remaining 67024 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.550
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:12.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6748
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      :  0.004   0.049   8510  Z= 0.262
  Angle     :  0.750   9.007  11565  Z= 0.396
  Chirality :  0.049   0.339   1362
  Planarity :  0.004   0.043   1445
  Dihedral  : 13.130  85.045   2988
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.23 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.46 (0.25), residues: 1072
  helix:  1.13 (0.27), residues: 355
  sheet: -0.04 (0.30), residues: 276
  loop : -1.68 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 164 
 HIS   0.017   0.002   HIS E 155 
 PHE   0.019   0.002   PHE C 278 
 TYR   0.023   0.002   TYR A 140 
 ARG   0.008   0.000   ARG C 219 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: E   95 TYR cc_start: 0.6503 (m-10) cc_final: 0.6295 (m-10)
REVERT: A  228 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.8610
  time to fit residues: 155.9774
Evaluate side-chains
  150 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0670
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 230 ASN
C 293 ASN
E 219 GLN
B 233 GLN
A 122 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.157303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.139753 restraints weight = 11425.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.94
r_work: 0.3778 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8510  Z= 0.242
  Angle     :  0.602   7.577  11565  Z= 0.319
  Chirality :  0.044   0.162   1362
  Planarity :  0.004   0.034   1445
  Dihedral  :  4.642  40.163   1239
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.23 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.12 (0.26), residues: 1072
  helix:  1.78 (0.28), residues: 349
  sheet: -0.05 (0.30), residues: 274
  loop : -1.63 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.022   0.002   PHE B 200 
 TYR   0.017   0.002   TYR A 140 
 ARG   0.007   0.001   ARG C 219 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7133 (pmt)
REVERT: E  180 MET cc_start: 0.5583 (ttp) cc_final: 0.5261 (ttp)
REVERT: B  309 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6788 (mp0)
REVERT: A  228 ILE cc_start: 0.7862 (mm) cc_final: 0.7622 (OUTLIER)
REVERT: A  332 PHE cc_start: 0.7961 (m-10) cc_final: 0.7707 (m-80)
  outliers start: 16
  outliers final: 3
  residues processed: 161
  average time/residue: 0.8907
  time to fit residues: 155.7623
Evaluate side-chains
  147 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain B residue  296 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 88 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 293 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.156190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.138565 restraints weight = 11638.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.96
r_work: 0.3766 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8510  Z= 0.264
  Angle     :  0.608   8.249  11565  Z= 0.318
  Chirality :  0.044   0.139   1362
  Planarity :  0.004   0.036   1445
  Dihedral  :  4.549  33.691   1239
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.12 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.03 (0.26), residues: 1072
  helix:  1.80 (0.28), residues: 351
  sheet:  0.07 (0.31), residues: 282
  loop : -1.63 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.021   0.002   PHE C 253 
 TYR   0.017   0.002   TYR A 140 
 ARG   0.004   0.000   ARG C  68 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7154 (pmt)
REVERT: E  180 MET cc_start: 0.5784 (ttp) cc_final: 0.5399 (ttp)
REVERT: E  201 THR cc_start: 0.7230 (p) cc_final: 0.7025 (t)
REVERT: E  208 GLU cc_start: 0.7755 (mp0) cc_final: 0.7249 (mp0)
REVERT: B  309 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6703 (mp0)
REVERT: A  107 LEU cc_start: 0.8157 (mt) cc_final: 0.7868 (mp)
REVERT: A  228 ILE cc_start: 0.7948 (mm) cc_final: 0.7735 (OUTLIER)
REVERT: A  332 PHE cc_start: 0.7937 (m-10) cc_final: 0.7673 (m-80)
  outliers start: 19
  outliers final: 7
  residues processed: 154
  average time/residue: 0.9542
  time to fit residues: 158.8404
Evaluate side-chains
  152 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 90 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 2 optimal weight:   20.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 268 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.156577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139291 restraints weight = 11569.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.89
r_work: 0.3778 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8510  Z= 0.223
  Angle     :  0.583   8.338  11565  Z= 0.304
  Chirality :  0.043   0.136   1362
  Planarity :  0.004   0.032   1445
  Dihedral  :  4.446  36.578   1239
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.61 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.05 (0.27), residues: 1072
  helix:  1.83 (0.28), residues: 358
  sheet:  0.12 (0.31), residues: 281
  loop : -1.60 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.016   0.002   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7160 (pmt)
REVERT: E  180 MET cc_start: 0.5721 (ttp) cc_final: 0.5366 (ttp)
REVERT: E  201 THR cc_start: 0.7233 (p) cc_final: 0.7030 (t)
REVERT: E  208 GLU cc_start: 0.7742 (mp0) cc_final: 0.7267 (mp0)
REVERT: B  309 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6674 (mp0)
REVERT: A  107 LEU cc_start: 0.8131 (mt) cc_final: 0.7880 (mp)
REVERT: A  169 PHE cc_start: 0.6688 (m-10) cc_final: 0.6422 (m-10)
REVERT: A  332 PHE cc_start: 0.7921 (m-10) cc_final: 0.7708 (m-80)
  outliers start: 25
  outliers final: 7
  residues processed: 174
  average time/residue: 0.8786
  time to fit residues: 166.5258
Evaluate side-chains
  156 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 147
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0010
   chunk 97 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0870
   overall best weight:    0.3964

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.157505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.140035 restraints weight = 11618.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.94
r_work: 0.3788 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8510  Z= 0.181
  Angle     :  0.562   8.690  11565  Z= 0.294
  Chirality :  0.042   0.146   1362
  Planarity :  0.003   0.032   1445
  Dihedral  :  4.312  36.190   1239
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.67 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.16 (0.27), residues: 1072
  helix:  1.97 (0.28), residues: 358
  sheet:  0.12 (0.31), residues: 280
  loop : -1.55 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.003   0.001   HIS B 189 
 PHE   0.013   0.001   PHE C 199 
 TYR   0.020   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.788 
Fit side-chains
REVERT: E  180 MET cc_start: 0.5619 (ttp) cc_final: 0.5282 (ttp)
REVERT: E  201 THR cc_start: 0.7242 (p) cc_final: 0.7020 (t)
REVERT: E  208 GLU cc_start: 0.7735 (mp0) cc_final: 0.7242 (mp0)
REVERT: B  309 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6578 (mp0)
REVERT: A  107 LEU cc_start: 0.8047 (mt) cc_final: 0.7772 (mp)
REVERT: A  112 MET cc_start: 0.3580 (mmt) cc_final: 0.2624 (mmp)
REVERT: A  169 PHE cc_start: 0.6699 (m-10) cc_final: 0.6444 (m-10)
REVERT: A  332 PHE cc_start: 0.7911 (m-10) cc_final: 0.7692 (m-80)
  outliers start: 23
  outliers final: 8
  residues processed: 172
  average time/residue: 0.8926
  time to fit residues: 167.6158
Evaluate side-chains
  164 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 74 optimal weight:    0.4980
   chunk 102 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 89 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.156362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.138888 restraints weight = 11566.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 1.95
r_work: 0.3771 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8510  Z= 0.236
  Angle     :  0.592   8.889  11565  Z= 0.309
  Chirality :  0.043   0.154   1362
  Planarity :  0.004   0.034   1445
  Dihedral  :  4.343  34.382   1239
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.59 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.10 (0.27), residues: 1072
  helix:  1.94 (0.28), residues: 358
  sheet:  0.11 (0.31), residues: 281
  loop : -1.61 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.018   0.002   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.008   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.875 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7176 (pmt)
REVERT: E  180 MET cc_start: 0.5623 (ttp) cc_final: 0.5247 (ttp)
REVERT: E  201 THR cc_start: 0.7234 (p) cc_final: 0.7022 (t)
REVERT: E  206 ARG cc_start: 0.7470 (mmp80) cc_final: 0.7016 (mmp80)
REVERT: E  208 GLU cc_start: 0.7772 (mp0) cc_final: 0.7250 (mp0)
REVERT: B  309 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6736 (mp0)
REVERT: A  107 LEU cc_start: 0.8035 (mt) cc_final: 0.7747 (mp)
REVERT: A  169 PHE cc_start: 0.6710 (m-10) cc_final: 0.6439 (m-10)
REVERT: A  332 PHE cc_start: 0.7946 (m-10) cc_final: 0.7726 (m-80)
  outliers start: 29
  outliers final: 11
  residues processed: 169
  average time/residue: 0.9440
  time to fit residues: 174.3660
Evaluate side-chains
  162 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0870
   chunk 77 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.5296

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.156892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139847 restraints weight = 11519.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.88
r_work: 0.3786 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3646 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8510  Z= 0.208
  Angle     :  0.582   9.074  11565  Z= 0.303
  Chirality :  0.042   0.157   1362
  Planarity :  0.004   0.046   1445
  Dihedral  :  4.294  32.660   1239
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.27 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.13 (0.27), residues: 1072
  helix:  1.99 (0.28), residues: 358
  sheet:  0.10 (0.31), residues: 281
  loop : -1.61 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.015   0.001   PHE C 253 
 TYR   0.020   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 0.944 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7157 (pmt)
REVERT: E  180 MET cc_start: 0.5515 (ttp) cc_final: 0.5172 (ttp)
REVERT: E  201 THR cc_start: 0.7231 (p) cc_final: 0.7018 (t)
REVERT: E  208 GLU cc_start: 0.7736 (mp0) cc_final: 0.7251 (mp0)
REVERT: B  309 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6729 (mp0)
REVERT: A  107 LEU cc_start: 0.8073 (mt) cc_final: 0.7772 (mp)
REVERT: A  169 PHE cc_start: 0.6716 (m-10) cc_final: 0.6443 (m-10)
  outliers start: 29
  outliers final: 16
  residues processed: 173
  average time/residue: 0.9014
  time to fit residues: 169.2253
Evaluate side-chains
  169 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  295 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0000
   chunk 5 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.156135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.138924 restraints weight = 11610.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 1.88
r_work: 0.3772 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8510  Z= 0.252
  Angle     :  0.612   9.122  11565  Z= 0.318
  Chirality :  0.043   0.165   1362
  Planarity :  0.004   0.042   1445
  Dihedral  :  4.402  31.509   1239
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.96 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.04 (0.26), residues: 1072
  helix:  1.82 (0.28), residues: 363
  sheet:  0.10 (0.31), residues: 280
  loop : -1.64 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.019   0.002   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.913 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7162 (pmt)
REVERT: E  180 MET cc_start: 0.5634 (ttp) cc_final: 0.5289 (ttp)
REVERT: E  201 THR cc_start: 0.7213 (p) cc_final: 0.7006 (t)
REVERT: E  206 ARG cc_start: 0.7474 (mmp80) cc_final: 0.7069 (mmp80)
REVERT: E  208 GLU cc_start: 0.7740 (mp0) cc_final: 0.7259 (mp0)
REVERT: B  309 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6831 (mp0)
REVERT: A  107 LEU cc_start: 0.8085 (mt) cc_final: 0.7798 (mp)
REVERT: A  112 MET cc_start: 0.3664 (mmp) cc_final: 0.3331 (mmp)
REVERT: A  169 PHE cc_start: 0.6738 (m-10) cc_final: 0.6444 (m-10)
  outliers start: 27
  outliers final: 19
  residues processed: 169
  average time/residue: 0.8873
  time to fit residues: 162.6268
Evaluate side-chains
  169 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  295 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 79 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.156615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.139378 restraints weight = 11649.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 1.90
r_work: 0.3773 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8510  Z= 0.223
  Angle     :  0.603   9.264  11565  Z= 0.312
  Chirality :  0.043   0.167   1362
  Planarity :  0.004   0.035   1445
  Dihedral  :  4.364  31.673   1239
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.19 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.02 (0.26), residues: 1072
  helix:  1.84 (0.28), residues: 364
  sheet:  0.07 (0.31), residues: 280
  loop : -1.68 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.016   0.002   PHE C 253 
 TYR   0.020   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.906 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7158 (pmt)
REVERT: E  180 MET cc_start: 0.5618 (ttp) cc_final: 0.5273 (ttp)
REVERT: E  201 THR cc_start: 0.7237 (p) cc_final: 0.7029 (t)
REVERT: E  206 ARG cc_start: 0.7458 (mmp80) cc_final: 0.7038 (mmp80)
REVERT: E  208 GLU cc_start: 0.7760 (mp0) cc_final: 0.7267 (mp0)
REVERT: B  309 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6735 (mp0)
REVERT: A  107 LEU cc_start: 0.8043 (mt) cc_final: 0.7743 (mp)
REVERT: A  169 PHE cc_start: 0.6723 (m-10) cc_final: 0.6447 (m-10)
  outliers start: 29
  outliers final: 19
  residues processed: 168
  average time/residue: 0.9426
  time to fit residues: 171.6708
Evaluate side-chains
  168 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 96 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:
C 155 ASN
C 220 GLN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.156270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.139004 restraints weight = 11590.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 1.90
r_work: 0.3776 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8510  Z= 0.240
  Angle     :  0.613   9.400  11565  Z= 0.319
  Chirality :  0.043   0.172   1362
  Planarity :  0.004   0.038   1445
  Dihedral  :  4.414  31.239   1239
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.08 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.00 (0.26), residues: 1072
  helix:  1.80 (0.27), residues: 364
  sheet:  0.05 (0.31), residues: 280
  loop : -1.67 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.018   0.002   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.960 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7164 (pmt)
REVERT: C  273 ILE cc_start: 0.7774 (mp) cc_final: 0.7573 (mp)
REVERT: E  180 MET cc_start: 0.5704 (ttp) cc_final: 0.5360 (ttp)
REVERT: E  201 THR cc_start: 0.7233 (p) cc_final: 0.7023 (t)
REVERT: E  206 ARG cc_start: 0.7478 (mmp80) cc_final: 0.7094 (mmp80)
REVERT: E  208 GLU cc_start: 0.7758 (mp0) cc_final: 0.7281 (mp0)
REVERT: B  309 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6811 (mp0)
REVERT: A  107 LEU cc_start: 0.8004 (mt) cc_final: 0.7698 (mp)
REVERT: A  112 MET cc_start: 0.3598 (mmp) cc_final: 0.2095 (mmp)
REVERT: A  169 PHE cc_start: 0.6745 (m-10) cc_final: 0.6475 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 163
  average time/residue: 0.8616
  time to fit residues: 152.6918
Evaluate side-chains
  167 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0370
   chunk 58 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
C 155 ASN
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.156701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.139432 restraints weight = 11619.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.91
r_work: 0.3778 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8510  Z= 0.230
  Angle     :  0.607   9.327  11565  Z= 0.315
  Chirality :  0.043   0.166   1362
  Planarity :  0.004   0.036   1445
  Dihedral  :  4.376  31.342   1239
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.19 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.02 (0.26), residues: 1072
  helix:  1.82 (0.27), residues: 364
  sheet:  0.07 (0.31), residues: 280
  loop : -1.66 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.016   0.002   PHE C 253 
 TYR   0.020   0.002   TYR A 140 
 ARG   0.008   0.000   ARG C 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6563.52 seconds
wall clock time: 116 minutes 37.02 seconds (6997.02 seconds total)