Starting phenix.real_space_refine
on Sat Jul 26 03:29:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dzq_27805/07_2025/8dzq_27805.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dzq_27805/07_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_27805/07_2025/8dzq_27805.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dzq_27805/07_2025/8dzq_27805.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dzq_27805/07_2025/8dzq_27805.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dzq_27805/07_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-5711/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: 5.77, per 1000 atoms: 0.69
  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.12
  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: 2.56

  Time building geometry restraints manager: 2.63 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:             1.310
  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:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.860
  Find NCS groups from input model:        0.090
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.270
-------------------------------------------------------------------------------
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   8512  Z= 0.183
  Angle     :  0.750   9.007  11569  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12438 (  441)
  hydrogen bonds       : angle       6.24164 ( 1233)
  SS BOND              : bond        0.00511 (    2)
  SS BOND              : angle       1.25708 (    4)
  covalent geometry    : bond        0.00403 ( 8510)
  covalent geometry    : angle       0.74976 (11565)

*********************** 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  : 0.909 
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: 0.8388
  time to fit residues: 151.9543
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  : 0.925 
-------------------------------------------------------------------------------
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 = 0.157289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139714 restraints weight = 11425.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.94
r_work: 0.3775 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
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   8512  Z= 0.163
  Angle     :  0.602   7.577  11569  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  441)
  hydrogen bonds       : angle       5.19568 ( 1233)
  SS BOND              : bond        0.00385 (    2)
  SS BOND              : angle       1.11616 (    4)
  covalent geometry    : bond        0.00367 ( 8510)
  covalent geometry    : angle       0.60179 (11565)

*********************** 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  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7144 (pmt)
REVERT: E  180 MET cc_start: 0.5596 (ttp) cc_final: 0.5273 (ttp)
REVERT: B  309 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6785 (mp0)
REVERT: A  228 ILE cc_start: 0.7861 (mm) cc_final: 0.7621 (OUTLIER)
REVERT: A  332 PHE cc_start: 0.7963 (m-10) cc_final: 0.7707 (m-80)
  outliers start: 16
  outliers final: 3
  residues processed: 161
  average time/residue: 0.8664
  time to fit residues: 151.5302
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  : 0.843 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.157108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.139573 restraints weight = 11657.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.95
r_work: 0.3781 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8512  Z= 0.146
  Angle     :  0.583   7.969  11569  Z= 0.305
  Chirality :  0.043   0.139   1362
  Planarity :  0.004   0.032   1445
  Dihedral  :  4.442  34.974   1239
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.55 %
    Favored  : 83.28 %
  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 (0.26), residues: 1072
  helix:  1.92 (0.28), residues: 350
  sheet:  0.09 (0.31), residues: 281
  loop : -1.61 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 169 
 HIS   0.004   0.001   HIS B 189 
 PHE   0.019   0.002   PHE B 200 
 TYR   0.018   0.002   TYR A 140 
 ARG   0.005   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04150 (  441)
  hydrogen bonds       : angle       5.02971 ( 1233)
  SS BOND              : bond        0.00326 (    2)
  SS BOND              : angle       0.86110 (    4)
  covalent geometry    : bond        0.00330 ( 8510)
  covalent geometry    : angle       0.58295 (11565)

*********************** 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
  170 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7158 (pmt)
REVERT: E  180 MET cc_start: 0.5592 (ttp) cc_final: 0.5252 (ttp)
REVERT: E  201 THR cc_start: 0.7232 (p) cc_final: 0.7020 (t)
REVERT: E  208 GLU cc_start: 0.7715 (mp0) cc_final: 0.7223 (mp0)
REVERT: B  309 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6693 (mp0)
REVERT: A  228 ILE cc_start: 0.7915 (mm) cc_final: 0.7698 (OUTLIER)
REVERT: A  332 PHE cc_start: 0.7938 (m-10) cc_final: 0.7678 (m-80)
  outliers start: 19
  outliers final: 7
  residues processed: 156
  average time/residue: 0.9427
  time to fit residues: 159.0151
Evaluate side-chains
  155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 33 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0870
   chunk 90 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 2 optimal weight:   20.0000
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN
A 322 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.157068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.139604 restraints weight = 11576.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.94
r_work: 0.3779 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8512  Z= 0.143
  Angle     :  0.578   8.350  11569  Z= 0.301
  Chirality :  0.043   0.145   1362
  Planarity :  0.004   0.031   1445
  Dihedral  :  4.373  36.007   1239
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.72 %
    Favored  : 80.76 %
  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:  1.93 (0.28), residues: 353
  sheet:  0.13 (0.31), residues: 281
  loop : -1.59 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 189 
 PHE   0.016   0.002   PHE C 253 
 TYR   0.018   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  441)
  hydrogen bonds       : angle       4.94108 ( 1233)
  SS BOND              : bond        0.00339 (    2)
  SS BOND              : angle       0.86877 (    4)
  covalent geometry    : bond        0.00323 ( 8510)
  covalent geometry    : angle       0.57787 (11565)

*********************** 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
  179 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7173 (pmt)
REVERT: E  180 MET cc_start: 0.5523 (ttp) cc_final: 0.5194 (ttp)
REVERT: E  201 THR cc_start: 0.7232 (p) cc_final: 0.7023 (t)
REVERT: E  208 GLU cc_start: 0.7742 (mp0) cc_final: 0.7237 (mp0)
REVERT: B  309 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6619 (mp0)
REVERT: A  107 LEU cc_start: 0.8120 (mt) cc_final: 0.7862 (mp)
REVERT: A  169 PHE cc_start: 0.6688 (m-10) cc_final: 0.6413 (m-10)
REVERT: A  332 PHE cc_start: 0.7931 (m-10) cc_final: 0.7671 (m-80)
  outliers start: 22
  outliers final: 6
  residues processed: 168
  average time/residue: 1.2922
  time to fit residues: 236.3697
Evaluate side-chains
  160 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  163 TYR
Chi-restraints excluded: chain B residue    6 SER
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:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0770
   chunk 97 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0970
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.4536

-------------------------------------------------------------------------------
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 = 0.157513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140283 restraints weight = 11620.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.89
r_work: 0.3790 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8512  Z= 0.130
  Angle     :  0.571   8.671  11569  Z= 0.298
  Chirality :  0.042   0.154   1362
  Planarity :  0.003   0.031   1445
  Dihedral  :  4.295  34.708   1239
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.21 %
    Favored  : 79.04 %
  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:  0.17 (0.27), residues: 1072
  helix:  2.01 (0.28), residues: 357
  sheet:  0.16 (0.31), residues: 280
  loop : -1.57 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 169 
 HIS   0.003   0.001   HIS B 189 
 PHE   0.014   0.001   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  441)
  hydrogen bonds       : angle       4.88750 ( 1233)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       0.73534 (    4)
  covalent geometry    : bond        0.00291 ( 8510)
  covalent geometry    : angle       0.57138 (11565)

*********************** 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
  176 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: E  208 GLU cc_start: 0.7737 (mp0) cc_final: 0.7255 (mp0)
REVERT: B  309 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6637 (mp0)
REVERT: A  107 LEU cc_start: 0.8070 (mt) cc_final: 0.7795 (mp)
REVERT: A  112 MET cc_start: 0.3452 (mmt) cc_final: 0.2648 (mmp)
REVERT: A  169 PHE cc_start: 0.6691 (m-10) cc_final: 0.6417 (m-10)
REVERT: A  332 PHE cc_start: 0.7933 (m-10) cc_final: 0.7721 (m-80)
  outliers start: 24
  outliers final: 12
  residues processed: 166
  average time/residue: 0.9826
  time to fit residues: 176.8944
Evaluate side-chains
  157 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  173 THR
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 E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
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  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
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:    0.0980
   chunk 88 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 102 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0040
   chunk 21 optimal weight:    0.0670
   chunk 81 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.2930

-------------------------------------------------------------------------------
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 189 HIS
** 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 = 0.4105 r_free = 0.4105 target = 0.158410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.141225 restraints weight = 11634.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 1.89
r_work: 0.3806 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3668 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8512  Z= 0.110
  Angle     :  0.553   8.887  11569  Z= 0.288
  Chirality :  0.042   0.155   1362
  Planarity :  0.003   0.030   1445
  Dihedral  :  4.149  36.096   1239
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.47 %
    Favored  : 77.89 %
  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:  0.25 (0.27), residues: 1072
  helix:  2.15 (0.28), residues: 357
  sheet:  0.13 (0.31), residues: 280
  loop : -1.56 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.004   0.001   HIS E 155 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.020   0.001   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  441)
  hydrogen bonds       : angle       4.77407 ( 1233)
  SS BOND              : bond        0.00302 (    2)
  SS BOND              : angle       0.55657 (    4)
  covalent geometry    : bond        0.00241 ( 8510)
  covalent geometry    : angle       0.55253 (11565)

*********************** 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
  174 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 151
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: E  208 GLU cc_start: 0.7704 (mp0) cc_final: 0.7241 (mp0)
REVERT: B  309 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6567 (mp0)
REVERT: A  107 LEU cc_start: 0.8037 (mt) cc_final: 0.7752 (mp)
REVERT: A  121 MET cc_start: 0.5477 (mpm) cc_final: 0.5021 (mpm)
  outliers start: 23
  outliers final: 9
  residues processed: 166
  average time/residue: 0.8548
  time to fit residues: 154.6601
Evaluate side-chains
  160 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  309 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0870
   chunk 77 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0470
   chunk 101 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0670
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.158393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.141215 restraints weight = 11610.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.88
r_work: 0.3805 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8512  Z= 0.116
  Angle     :  0.562   9.027  11569  Z= 0.293
  Chirality :  0.042   0.164   1362
  Planarity :  0.003   0.041   1445
  Dihedral  :  4.098  33.279   1239
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.96 %
    Favored  : 76.29 %
  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:  0.29 (0.27), residues: 1072
  helix:  2.20 (0.28), residues: 357
  sheet:  0.14 (0.31), residues: 280
  loop : -1.55 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 124 
 HIS   0.003   0.001   HIS E 155 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.020   0.001   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  441)
  hydrogen bonds       : angle       4.74359 ( 1233)
  SS BOND              : bond        0.00318 (    2)
  SS BOND              : angle       0.65187 (    4)
  covalent geometry    : bond        0.00259 ( 8510)
  covalent geometry    : angle       0.56208 (11565)

*********************** 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
  181 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
REVERT: C   61 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7639 (ppp)
REVERT: C   76 ASP cc_start: 0.7966 (p0) cc_final: 0.7714 (p0)
REVERT: C  217 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7210 (pmt)
REVERT: E  208 GLU cc_start: 0.7695 (mp0) cc_final: 0.7229 (mp0)
REVERT: B  309 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6678 (mp0)
REVERT: A  107 LEU cc_start: 0.8054 (mt) cc_final: 0.7749 (mp)
  outliers start: 24
  outliers final: 12
  residues processed: 171
  average time/residue: 0.9495
  time to fit residues: 175.2903
Evaluate side-chains
  161 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   61 MET
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 E residue    7 SER
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain B residue    6 SER
Chi-restraints excluded: chain B residue   13 LEU
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  122 ASN
Chi-restraints excluded: chain A residue  256 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:   20.0000
   chunk 15 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:
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.156421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.139143 restraints weight = 11567.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.89
r_work: 0.3779 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8512  Z= 0.174
  Angle     :  0.617   8.967  11569  Z= 0.321
  Chirality :  0.044   0.166   1362
  Planarity :  0.004   0.037   1445
  Dihedral  :  4.329  31.856   1239
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.42 %
    Favored  : 75.26 %
  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 (0.26), residues: 1072
  helix:  1.86 (0.28), residues: 364
  sheet:  0.15 (0.31), residues: 280
  loop : -1.62 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 124 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.021   0.002   PHE C 253 
 TYR   0.018   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04128 (  441)
  hydrogen bonds       : angle       4.88231 ( 1233)
  SS BOND              : bond        0.00301 (    2)
  SS BOND              : angle       1.32651 (    4)
  covalent geometry    : bond        0.00405 ( 8510)
  covalent geometry    : angle       0.61617 (11565)

*********************** 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
  168 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 1.380 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7208 (pmt)
REVERT: E  208 GLU cc_start: 0.7743 (mp0) cc_final: 0.7251 (mp0)
REVERT: B  309 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6835 (mp0)
REVERT: A  107 LEU cc_start: 0.8085 (mt) cc_final: 0.7760 (mp)
REVERT: A  121 MET cc_start: 0.5554 (mpm) cc_final: 0.5187 (mpm)
  outliers start: 29
  outliers final: 16
  residues processed: 156
  average time/residue: 0.9536
  time to fit residues: 161.3519
Evaluate side-chains
  161 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
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  234 PHE
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  261 LEU
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  153 SER
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   chunk 3 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 49 optimal weight:    0.4980
   chunk 6 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:
E 219 GLN
** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.156837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.139541 restraints weight = 11636.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.89
r_work: 0.3781 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8512  Z= 0.160
  Angle     :  0.614   9.439  11569  Z= 0.319
  Chirality :  0.043   0.173   1362
  Planarity :  0.004   0.032   1445
  Dihedral  :  4.328  31.171   1239
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.53 %
    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:  0.05 (0.26), residues: 1072
  helix:  1.84 (0.28), residues: 364
  sheet:  0.09 (0.31), residues: 280
  loop : -1.64 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 124 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.002   PHE C 253 
 TYR   0.019   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  441)
  hydrogen bonds       : angle       4.87753 ( 1233)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       1.31136 (    4)
  covalent geometry    : bond        0.00370 ( 8510)
  covalent geometry    : angle       0.61360 (11565)

*********************** 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
  177 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: C  217 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7212 (pmt)
REVERT: E  208 GLU cc_start: 0.7728 (mp0) cc_final: 0.7251 (mp0)
REVERT: B  309 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6827 (mp0)
REVERT: A   81 MET cc_start: 0.6622 (mmt) cc_final: 0.6377 (mmt)
REVERT: A  107 LEU cc_start: 0.8008 (mt) cc_final: 0.7677 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 167
  average time/residue: 0.9231
  time to fit residues: 166.7922
Evaluate side-chains
  164 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
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  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  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  153 SER
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
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:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.155638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138395 restraints weight = 11533.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 1.89
r_work: 0.3766 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3623 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   8512  Z= 0.201
  Angle     :  0.656  10.925  11569  Z= 0.340
  Chirality :  0.045   0.177   1362
  Planarity :  0.004   0.043   1445
  Dihedral  :  4.528  29.735   1239
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.53 %
    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: -0.05 (0.26), residues: 1072
  helix:  1.74 (0.27), residues: 361
  sheet:  0.11 (0.31), residues: 277
  loop : -1.71 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 124 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.023   0.002   PHE C 253 
 TYR   0.018   0.002   TYR A 140 
 ARG   0.008   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  441)
  hydrogen bonds       : angle       5.01588 ( 1233)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       1.38758 (    4)
  covalent geometry    : bond        0.00471 ( 8510)
  covalent geometry    : angle       0.65557 (11565)

********************** 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
  171 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.956 
Fit side-chains
REVERT: C  217 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7216 (pmt)
REVERT: C  273 ILE cc_start: 0.7742 (mp) cc_final: 0.7503 (mp)
REVERT: E  206 ARG cc_start: 0.7493 (mmp80) cc_final: 0.7022 (mmp80)
REVERT: E  208 GLU cc_start: 0.7750 (mp0) cc_final: 0.7268 (mp0)
REVERT: B  309 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6876 (mp0)
REVERT: A  107 LEU cc_start: 0.8024 (mt) cc_final: 0.7682 (mp)
REVERT: A  112 MET cc_start: 0.3698 (mmp) cc_final: 0.2393 (mmp)
  outliers start: 24
  outliers final: 18
  residues processed: 163
  average time/residue: 0.9413
  time to fit residues: 165.7322
Evaluate side-chains
  162 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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  153 SER
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
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:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0570
   chunk 58 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0040
   chunk 1 optimal weight:   10.0000
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.4710

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.157084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.139862 restraints weight = 11625.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.90
r_work: 0.3786 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8512  Z= 0.139
  Angle     :  0.612  10.704  11569  Z= 0.317
  Chirality :  0.043   0.164   1362
  Planarity :  0.004   0.031   1445
  Dihedral  :  4.360  30.878   1239
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 22.45 %
    Favored  : 75.03 %
  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: -0.01 (0.26), residues: 1072
  helix:  1.80 (0.27), residues: 364
  sheet:  0.04 (0.31), residues: 280
  loop : -1.67 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 124 
 HIS   0.003   0.001   HIS B 189 
 PHE   0.015   0.001   PHE C 253 
 TYR   0.021   0.002   TYR A 140 
 ARG   0.007   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  441)
  hydrogen bonds       : angle       4.90466 ( 1233)
  SS BOND              : bond        0.00367 (    2)
  SS BOND              : angle       0.82295 (    4)
  covalent geometry    : bond        0.00318 ( 8510)
  covalent geometry    : angle       0.61173 (11565)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7800.43 seconds
wall clock time: 139 minutes 23.94 seconds (8363.94 seconds total)