Starting phenix.real_space_refine
on Fri Jun  6 07:25:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hj2_33481/06_2025/8hj2_33481.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.002
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      40      5.16       5
     C    4712      2.51       5
     N    1306      2.21       5
     O    1409      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7467
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2423
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 144
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 86
    Chain: "G"
      Number of atoms: 230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 230
          Classifications: {'peptide': 46}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 4, 'TRANS': 41}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 67
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 1966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 1966
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 103}
          Link IDs: {'PTRANS': 10, 'TRANS': 271}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 341
          Unresolved non-hydrogen angles: 442
          Unresolved non-hydrogen dihedrals: 284
          Unresolved non-hydrogen chiralities: 43
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 165
    Chain: "A"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1887
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 95
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 55
  Time building chain proxies: 6.80, per 1000 atoms: 0.91
  Number of scatterers: 7467
  At special positions: 0
  Unit cell: (85.696, 102.336, 119.808, 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      40     16.00
     O    1409      8.00
     N    1306      7.00
     C    4712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 122 " - pdb=" SG  CYS R 149 " distance=2.06

  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: 2.10
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      41.0% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 18 through 24
      removed outlier: 4.180A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.057A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.844A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 56
      removed outlier: 6.083A  pdb=" N   ILE R  34 " --> pdb=" O   LEU R  30 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ILE R  35 " --> pdb=" O   GLU R  31 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU R  41 " --> pdb=" O   PHE R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 63 through 91
      removed outlier: 4.067A  pdb=" N   PHE R  67 " --> pdb=" O   THR R  63 " (cutoff:3.500A)
      Proline residue:  R  85  - end of helix
      removed outlier: 3.931A  pdb=" N   LEU R  90 " --> pdb=" O   SER R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 133
      removed outlier: 3.661A  pdb=" N   PHE R 105 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE R 107 " --> pdb=" O   GLN R 103 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER R 114 " --> pdb=" O   SER R 110 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 141
    Processing helix  chain 'R' and resid 142 through 162
      removed outlier: 4.301A  pdb=" N   PHE R 161 " --> pdb=" O   SER R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 163 through 165
      No H-bonds generated for 'chain 'R' and resid 163 through 165'
    Processing helix  chain 'R' and resid 178 through 184
    Processing helix  chain 'R' and resid 188 through 197
    Processing helix  chain 'R' and resid 199 through 232
      removed outlier: 3.847A  pdb=" N   PHE R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 279
      Proline residue:  R 267  - end of helix
    Processing helix  chain 'R' and resid 282 through 295
    Processing helix  chain 'R' and resid 295 through 308
      removed outlier: 4.438A  pdb=" N   CYS R 301 " --> pdb=" O   SER R 297 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   VAL R 302 " --> pdb=" O   PHE R 298 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 323
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 4.074A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.590A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 283 through 293
      removed outlier: 3.527A  pdb=" N   LEU A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.301A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 3.641A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 321 through 340
      removed outlier: 3.803A  pdb=" N   THR A 325 " --> pdb=" O   ASP A 321 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 384
      removed outlier: 3.574A  pdb=" N   ARG A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASN A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.513A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.529A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.068A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 151
      removed outlier: 7.005A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.585A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.447A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.885A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.340A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 5.969A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.598A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1167 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: 2.61

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 2487
        1.35 -     1.48: 2049
        1.48 -     1.62: 3027
        1.62 -     1.75: 0
        1.75 -     1.88: 54
  Bond restraints: 7617
  Sorted by residual:
  bond pdb=" CB  CYS R 149 "
       pdb=" SG  CYS R 149 "
    ideal  model  delta    sigma   weight residual
    1.808  1.884 -0.076 3.30e-02 9.18e+02 5.35e+00
  bond pdb=" CB  CYS R 122 "
       pdb=" SG  CYS R 122 "
    ideal  model  delta    sigma   weight residual
    1.808  1.884 -0.076 3.30e-02 9.18e+02 5.29e+00
  bond pdb=" CB  VAL B 296 "
       pdb=" CG2 VAL B 296 "
    ideal  model  delta    sigma   weight residual
    1.521  1.449  0.072 3.30e-02 9.18e+02 4.77e+00
  bond pdb=" CB  VAL R 207 "
       pdb=" CG1 VAL R 207 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.61e+00
  bond pdb=" CA  ALA B 231 "
       pdb=" CB  ALA B 231 "
    ideal  model  delta    sigma   weight residual
    1.534  1.498  0.036 1.78e-02 3.16e+03 4.08e+00
  ... (remaining 7612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 10176
        3.58 -     7.15: 182
        7.15 -    10.73: 18
       10.73 -    14.30: 2
       14.30 -    17.88: 2
  Bond angle restraints: 10380
  Sorted by residual:
  angle pdb=" CG  ARG R 147 "
        pdb=" CD  ARG R 147 "
        pdb=" NE  ARG R 147 "
      ideal   model   delta    sigma   weight residual
     112.00  129.88  -17.88 2.20e+00 2.07e-01 6.61e+01
  angle pdb=" N   THR A 315 "
        pdb=" CA  THR A 315 "
        pdb=" C   THR A 315 "
      ideal   model   delta    sigma   weight residual
     109.81  122.54  -12.73 2.21e+00 2.05e-01 3.32e+01
  angle pdb=" C   LEU R 140 "
        pdb=" N   VAL R 141 "
        pdb=" CA  VAL R 141 "
      ideal   model   delta    sigma   weight residual
     121.65  116.60    5.05 9.40e-01 1.13e+00 2.89e+01
  angle pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
        pdb=" C   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     106.21  111.13   -4.92 1.07e+00 8.73e-01 2.11e+01
  angle pdb=" CA  ARG R 147 "
        pdb=" CB  ARG R 147 "
        pdb=" CG  ARG R 147 "
      ideal   model   delta    sigma   weight residual
     114.10  122.91   -8.81 2.00e+00 2.50e-01 1.94e+01
  ... (remaining 10375 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 4050
       17.38 -    34.76: 349
       34.76 -    52.14: 44
       52.14 -    69.51: 5
       69.51 -    86.89: 6
  Dihedral angle restraints: 4454
    sinusoidal: 1465
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CB  CYS R 122 "
           pdb=" SG  CYS R 122 "
           pdb=" SG  CYS R 149 "
           pdb=" CB  CYS R 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.89  -86.89     1      1.00e+01 1.00e-02 9.08e+01
  dihedral pdb=" CA  VAL R 111 "
           pdb=" C   VAL R 111 "
           pdb=" N   LEU R 112 "
           pdb=" CA  LEU R 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.69  -27.31     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  ASN B 237 "
           pdb=" C   ASN B 237 "
           pdb=" N   GLY B 238 "
           pdb=" CA  GLY B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.00   27.00     0      5.00e+00 4.00e-02 2.92e+01
  ... (remaining 4451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1052
       0.096 -    0.192: 133
       0.192 -    0.288: 10
       0.288 -    0.383: 3
       0.383 -    0.479: 1
  Chirality restraints: 1199
  Sorted by residual:
  chirality pdb=" CB  ILE B 123 "
            pdb=" CA  ILE B 123 "
            pdb=" CG1 ILE B 123 "
            pdb=" CG2 ILE B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.48 2.00e-01 2.50e+01 5.74e+00
  chirality pdb=" CG  LEU N  45 "
            pdb=" CB  LEU N  45 "
            pdb=" CD1 LEU N  45 "
            pdb=" CD2 LEU N  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.23   -0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.44e+00
  ... (remaining 1196 not shown)

  Planarity restraints: 1341
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 321 "    0.065 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO A 322 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 169 "    0.030 2.00e-02 2.50e+03   2.15e-02 1.15e+01
        pdb=" CG  TRP B 169 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 169 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 169 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 169 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 169 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 169 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 350 "   -0.019 2.00e-02 2.50e+03   2.22e-02 9.86e+00
        pdb=" CG  TYR A 350 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 350 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 350 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 350 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 350 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 350 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 350 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1338 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1625
        2.77 -     3.31: 7265
        3.31 -     3.84: 12585
        3.84 -     4.37: 14090
        4.37 -     4.90: 24254
  Nonbonded interactions: 59819
  Sorted by model distance:
  nonbonded pdb=" O   SER R 116 "
            pdb=" OG  SER R 119 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   VAL R 111 "
            pdb=" OG  SER R 114 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   ASP B 228 "
            pdb=" OG  SER B 245 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG1 THR N  91 "
            pdb=" O   VAL N 124 "
     model   vdw
     2.312 3.040
  ... (remaining 59814 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 group one per residue
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:             40.000
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     33.340
  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:5.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   79.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
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      :  0.007   0.076   7620  Z= 0.345
  Angle     :  1.207  17.880  10386  Z= 0.667
  Chirality :  0.066   0.479   1199
  Planarity :  0.008   0.101   1341
  Dihedral  : 13.410  82.535   2511
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.23), residues: 1013
  helix: -1.03 (0.21), residues: 400
  sheet: -0.66 (0.35), residues: 214
  loop : -2.24 (0.27), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.005   TRP B 169 
 HIS   0.010   0.003   HIS A 347 
 PHE   0.044   0.004   PHE N  29 
 TYR   0.054   0.004   TYR A 350 
 ARG   0.023   0.002   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15092 (  402)
  hydrogen bonds       : angle       7.38056 ( 1167)
  SS BOND              : bond        0.01544 (    3)
  SS BOND              : angle       3.90102 (    6)
  covalent geometry    : bond        0.00749 ( 7617)
  covalent geometry    : angle       1.20323 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: B  280 LYS cc_start: 0.7598 (tttt) cc_final: 0.7239 (ttmt)
REVERT: B  293 ASN cc_start: 0.8829 (p0) cc_final: 0.8589 (p0)
REVERT: N   60 TYR cc_start: 0.7306 (m-80) cc_final: 0.6746 (m-80)
REVERT: A  209 GLU cc_start: 0.7146 (pp20) cc_final: 0.6860 (pp20)
REVERT: A  252 ASP cc_start: 0.8020 (t0) cc_final: 0.7664 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 310
  average time/residue: 0.2397
  time to fit residues: 95.7108
Evaluate side-chains
  277 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.0770
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
B 176 GLN
R 213 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 ASN
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.162226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.135251 restraints weight = 12318.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139518 restraints weight = 6881.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142497 restraints weight = 4502.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7620  Z= 0.145
  Angle     :  0.642   8.031  10386  Z= 0.341
  Chirality :  0.045   0.167   1199
  Planarity :  0.005   0.066   1341
  Dihedral  :  5.563  20.275   1100
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.77 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.25), residues: 1013
  helix:  0.82 (0.25), residues: 409
  sheet: -0.36 (0.35), residues: 218
  loop : -2.00 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 169 
 HIS   0.005   0.001   HIS R 174 
 PHE   0.022   0.002   PHE R 272 
 TYR   0.016   0.001   TYR B  85 
 ARG   0.007   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04555 (  402)
  hydrogen bonds       : angle       5.22190 ( 1167)
  SS BOND              : bond        0.00886 (    3)
  SS BOND              : angle       2.80800 (    6)
  covalent geometry    : bond        0.00313 ( 7617)
  covalent geometry    : angle       0.63890 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 292
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  241 PHE cc_start: 0.8615 (p90) cc_final: 0.8299 (p90)
REVERT: B  262 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.7172 (mmt)
REVERT: N   34 MET cc_start: 0.7708 (mmm) cc_final: 0.7409 (mmt)
REVERT: N   60 TYR cc_start: 0.7668 (m-80) cc_final: 0.7131 (m-80)
REVERT: N   67 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6241 (ttp80)
REVERT: R  137 TYR cc_start: 0.8723 (t80) cc_final: 0.7930 (t80)
REVERT: R  153 ILE cc_start: 0.8963 (mt) cc_final: 0.8759 (mt)
REVERT: A  209 GLU cc_start: 0.6994 (pp20) cc_final: 0.6663 (pp20)
REVERT: A  220 HIS cc_start: 0.8035 (t70) cc_final: 0.7336 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 298
  average time/residue: 0.1951
  time to fit residues: 77.3239
Evaluate side-chains
  301 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 284
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:   30.0000
   chunk 4 optimal weight:    8.9990
   chunk 96 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.158684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133496 restraints weight = 12505.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.137633 restraints weight = 6799.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.140273 restraints weight = 4358.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7620  Z= 0.165
  Angle     :  0.623   7.995  10386  Z= 0.336
  Chirality :  0.044   0.169   1199
  Planarity :  0.004   0.044   1341
  Dihedral  :  5.160  17.724   1100
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 17.10 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1013
  helix:  1.55 (0.26), residues: 402
  sheet: -0.36 (0.35), residues: 217
  loop : -1.89 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.015   0.002   PHE R 191 
 TYR   0.013   0.002   TYR B  85 
 ARG   0.008   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  402)
  hydrogen bonds       : angle       4.92452 ( 1167)
  SS BOND              : bond        0.00762 (    3)
  SS BOND              : angle       2.41119 (    6)
  covalent geometry    : bond        0.00365 ( 7617)
  covalent geometry    : angle       0.62019 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 295
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ILE cc_start: 0.8763 (mp) cc_final: 0.8558 (mp)
REVERT: B  124 TYR cc_start: 0.7961 (m-80) cc_final: 0.7617 (m-80)
REVERT: B  205 ASP cc_start: 0.8401 (p0) cc_final: 0.8170 (p0)
REVERT: B  241 PHE cc_start: 0.8624 (p90) cc_final: 0.8329 (p90)
REVERT: N    3 GLN cc_start: 0.6837 (tt0) cc_final: 0.6575 (tm-30)
REVERT: N   34 MET cc_start: 0.7933 (mmm) cc_final: 0.7639 (mmt)
REVERT: N   60 TYR cc_start: 0.7739 (m-80) cc_final: 0.7337 (m-80)
REVERT: N   67 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6780 (ttp80)
REVERT: N   87 LYS cc_start: 0.7964 (tttt) cc_final: 0.7421 (tttt)
REVERT: R  126 ASP cc_start: 0.8790 (t0) cc_final: 0.8557 (t0)
REVERT: R  137 TYR cc_start: 0.8776 (t80) cc_final: 0.8045 (t80)
REVERT: R  153 ILE cc_start: 0.8912 (mt) cc_final: 0.8693 (mt)
REVERT: R  170 LYS cc_start: 0.7580 (mttm) cc_final: 0.7371 (mttp)
REVERT: R  217 ILE cc_start: 0.8710 (mm) cc_final: 0.8479 (mt)
REVERT: R  275 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7097 (tt0)
REVERT: A  209 GLU cc_start: 0.7039 (pp20) cc_final: 0.6545 (pp20)
REVERT: A  220 HIS cc_start: 0.8044 (t70) cc_final: 0.7261 (t70)
  outliers start: 35
  outliers final: 20
  residues processed: 304
  average time/residue: 0.1941
  time to fit residues: 78.1870
Evaluate side-chains
  303 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 282
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   67 ARG
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 94 optimal weight:    5.9990
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
B 176 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.154871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.129645 restraints weight = 12635.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133614 restraints weight = 6948.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136339 restraints weight = 4517.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   7620  Z= 0.229
  Angle     :  0.681  12.365  10386  Z= 0.367
  Chirality :  0.046   0.160   1199
  Planarity :  0.005   0.043   1341
  Dihedral  :  5.255  17.462   1100
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 18.26 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1013
  helix:  1.62 (0.26), residues: 403
  sheet: -0.31 (0.35), residues: 214
  loop : -2.02 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.028   0.002   PHE N  29 
 TYR   0.019   0.002   TYR R 211 
 ARG   0.004   0.001   ARG A 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04647 (  402)
  hydrogen bonds       : angle       5.02709 ( 1167)
  SS BOND              : bond        0.00919 (    3)
  SS BOND              : angle       2.52643 (    6)
  covalent geometry    : bond        0.00499 ( 7617)
  covalent geometry    : angle       0.67801 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 281
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8578 (mp)
REVERT: B  124 TYR cc_start: 0.7964 (m-80) cc_final: 0.7625 (m-80)
REVERT: B  156 GLN cc_start: 0.7781 (mt0) cc_final: 0.7544 (mt0)
REVERT: B  205 ASP cc_start: 0.8419 (p0) cc_final: 0.8203 (p0)
REVERT: B  241 PHE cc_start: 0.8744 (p90) cc_final: 0.8442 (p90)
REVERT: N    3 GLN cc_start: 0.6809 (tt0) cc_final: 0.6554 (tm-30)
REVERT: N   34 MET cc_start: 0.8034 (mmm) cc_final: 0.7661 (mmt)
REVERT: N   60 TYR cc_start: 0.7723 (m-80) cc_final: 0.7424 (m-80)
REVERT: N  115 TYR cc_start: 0.7852 (t80) cc_final: 0.7420 (t80)
REVERT: R  137 TYR cc_start: 0.8823 (t80) cc_final: 0.8088 (t80)
REVERT: R  153 ILE cc_start: 0.8932 (mt) cc_final: 0.8704 (mt)
REVERT: R  198 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6944 (mpt)
REVERT: R  211 TYR cc_start: 0.7766 (m-80) cc_final: 0.7408 (t80)
REVERT: R  217 ILE cc_start: 0.8668 (mm) cc_final: 0.8436 (mt)
  outliers start: 48
  outliers final: 35
  residues processed: 299
  average time/residue: 0.1977
  time to fit residues: 78.1983
Evaluate side-chains
  314 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 277
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  381 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0070
   chunk 80 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.132967 restraints weight = 12484.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.137051 restraints weight = 6850.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139716 restraints weight = 4439.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7620  Z= 0.151
  Angle     :  0.622   9.391  10386  Z= 0.331
  Chirality :  0.044   0.156   1199
  Planarity :  0.004   0.046   1341
  Dihedral  :  4.893  17.185   1100
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 20.43 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.27), residues: 1013
  helix:  2.10 (0.26), residues: 397
  sheet: -0.33 (0.35), residues: 211
  loop : -1.97 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.031   0.002   PHE N  29 
 TYR   0.020   0.001   TYR R 211 
 ARG   0.004   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  402)
  hydrogen bonds       : angle       4.71560 ( 1167)
  SS BOND              : bond        0.00681 (    3)
  SS BOND              : angle       2.12915 (    6)
  covalent geometry    : bond        0.00335 ( 7617)
  covalent geometry    : angle       0.61959 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 280
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.8037 (m-80) cc_final: 0.7690 (m-80)
REVERT: B  205 ASP cc_start: 0.8320 (p0) cc_final: 0.8105 (p0)
REVERT: B  241 PHE cc_start: 0.8719 (p90) cc_final: 0.8415 (p90)
REVERT: B  251 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7415 (mtm-85)
REVERT: B  280 LYS cc_start: 0.7559 (tttt) cc_final: 0.7306 (ttmt)
REVERT: N    3 GLN cc_start: 0.6815 (tt0) cc_final: 0.6549 (tm-30)
REVERT: N   34 MET cc_start: 0.8008 (mmm) cc_final: 0.7624 (mmt)
REVERT: N   60 TYR cc_start: 0.7731 (m-80) cc_final: 0.7436 (m-80)
REVERT: N  115 TYR cc_start: 0.7807 (t80) cc_final: 0.7392 (t80)
REVERT: R  137 TYR cc_start: 0.8785 (t80) cc_final: 0.7956 (t80)
REVERT: R  153 ILE cc_start: 0.8864 (mt) cc_final: 0.8640 (mt)
REVERT: R  198 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6727 (mpt)
REVERT: R  211 TYR cc_start: 0.7759 (m-80) cc_final: 0.7424 (t80)
REVERT: R  217 ILE cc_start: 0.8703 (mm) cc_final: 0.8470 (mt)
REVERT: A  263 PHE cc_start: 0.9303 (t80) cc_final: 0.9050 (t80)
  outliers start: 38
  outliers final: 26
  residues processed: 292
  average time/residue: 0.1917
  time to fit residues: 74.0281
Evaluate side-chains
  298 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 271
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 2 optimal weight:   20.0000
   chunk 64 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.132524 restraints weight = 12770.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.136657 restraints weight = 6998.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139362 restraints weight = 4536.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7620  Z= 0.171
  Angle     :  0.635   9.328  10386  Z= 0.340
  Chirality :  0.045   0.153   1199
  Planarity :  0.004   0.046   1341
  Dihedral  :  4.859  17.002   1100
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 21.59 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.27), residues: 1013
  helix:  1.97 (0.26), residues: 409
  sheet: -0.23 (0.35), residues: 211
  loop : -1.94 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.019   0.002   PHE B 199 
 TYR   0.020   0.002   TYR A  37 
 ARG   0.003   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  402)
  hydrogen bonds       : angle       4.73450 ( 1167)
  SS BOND              : bond        0.00744 (    3)
  SS BOND              : angle       2.04855 (    6)
  covalent geometry    : bond        0.00380 ( 7617)
  covalent geometry    : angle       0.63364 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 271
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.8075 (m-80) cc_final: 0.7721 (m-80)
REVERT: B  205 ASP cc_start: 0.8377 (p0) cc_final: 0.8157 (p0)
REVERT: B  241 PHE cc_start: 0.8742 (p90) cc_final: 0.8527 (p90)
REVERT: B  280 LYS cc_start: 0.7554 (tttt) cc_final: 0.7267 (ttmt)
REVERT: B  301 LYS cc_start: 0.7452 (mptt) cc_final: 0.7077 (mttm)
REVERT: N    3 GLN cc_start: 0.6833 (tt0) cc_final: 0.6553 (tm-30)
REVERT: N   34 MET cc_start: 0.8033 (mmm) cc_final: 0.7678 (mmt)
REVERT: N   60 TYR cc_start: 0.7713 (m-80) cc_final: 0.7504 (m-80)
REVERT: N  115 TYR cc_start: 0.7792 (t80) cc_final: 0.7313 (t80)
REVERT: R  137 TYR cc_start: 0.8781 (t80) cc_final: 0.7962 (t80)
REVERT: R  153 ILE cc_start: 0.8859 (mt) cc_final: 0.8631 (mt)
REVERT: R  170 LYS cc_start: 0.7629 (mttm) cc_final: 0.7375 (mttp)
REVERT: R  198 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6791 (mpt)
REVERT: R  211 TYR cc_start: 0.7693 (m-80) cc_final: 0.7414 (t80)
REVERT: R  217 ILE cc_start: 0.8699 (mm) cc_final: 0.8465 (mt)
REVERT: A  263 PHE cc_start: 0.9322 (t80) cc_final: 0.9062 (t80)
  outliers start: 40
  outliers final: 28
  residues processed: 285
  average time/residue: 0.1962
  time to fit residues: 74.2864
Evaluate side-chains
  296 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 267
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  111 VAL
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain R residue  275 GLU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0000
   chunk 78 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
A 367 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.159081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133376 restraints weight = 12646.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.137483 restraints weight = 6926.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.140148 restraints weight = 4489.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7620  Z= 0.164
  Angle     :  0.635  12.443  10386  Z= 0.337
  Chirality :  0.045   0.159   1199
  Planarity :  0.004   0.048   1341
  Dihedral  :  4.762  16.814   1100
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 24.06 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 1013
  helix:  2.00 (0.26), residues: 409
  sheet: -0.17 (0.35), residues: 213
  loop : -1.94 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.016   0.002   PHE R 191 
 TYR   0.018   0.002   TYR A  37 
 ARG   0.002   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04059 (  402)
  hydrogen bonds       : angle       4.71740 ( 1167)
  SS BOND              : bond        0.00728 (    3)
  SS BOND              : angle       1.93730 (    6)
  covalent geometry    : bond        0.00370 ( 7617)
  covalent geometry    : angle       0.63342 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 272
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7788 (mp10)
REVERT: B  124 TYR cc_start: 0.8064 (m-80) cc_final: 0.7629 (m-80)
REVERT: B  205 ASP cc_start: 0.8345 (p0) cc_final: 0.8122 (p0)
REVERT: B  251 ARG cc_start: 0.7829 (mtt90) cc_final: 0.7472 (mtm-85)
REVERT: B  301 LYS cc_start: 0.7451 (mptt) cc_final: 0.7069 (mttm)
REVERT: N    3 GLN cc_start: 0.6884 (tt0) cc_final: 0.6608 (tm-30)
REVERT: N   34 MET cc_start: 0.8120 (mmm) cc_final: 0.7781 (mmt)
REVERT: N   60 TYR cc_start: 0.7667 (m-80) cc_final: 0.7462 (m-80)
REVERT: N  115 TYR cc_start: 0.7793 (t80) cc_final: 0.7336 (t80)
REVERT: R  137 TYR cc_start: 0.8774 (t80) cc_final: 0.7903 (t80)
REVERT: R  153 ILE cc_start: 0.8833 (mt) cc_final: 0.8601 (mt)
REVERT: R  170 LYS cc_start: 0.7636 (mttm) cc_final: 0.7353 (mttp)
REVERT: R  198 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6752 (mpt)
REVERT: R  211 TYR cc_start: 0.7704 (m-80) cc_final: 0.7469 (t80)
REVERT: R  217 ILE cc_start: 0.8730 (mm) cc_final: 0.8487 (mt)
REVERT: A  263 PHE cc_start: 0.9311 (t80) cc_final: 0.9069 (t80)
  outliers start: 33
  outliers final: 26
  residues processed: 283
  average time/residue: 0.1937
  time to fit residues: 72.6637
Evaluate side-chains
  296 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 268
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue  108 VAL
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  146 LEU
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0370
   chunk 57 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
A 284 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.162584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.137161 restraints weight = 12519.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.141462 restraints weight = 6786.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.144373 restraints weight = 4329.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7620  Z= 0.126
  Angle     :  0.617  12.322  10386  Z= 0.322
  Chirality :  0.044   0.182   1199
  Planarity :  0.004   0.049   1341
  Dihedral  :  4.510  17.101   1100
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 25.36 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.27), residues: 1013
  helix:  2.37 (0.26), residues: 399
  sheet: -0.18 (0.35), residues: 221
  loop : -1.86 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 297 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.015   0.001   PHE R 191 
 TYR   0.019   0.001   TYR A  37 
 ARG   0.003   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  402)
  hydrogen bonds       : angle       4.51253 ( 1167)
  SS BOND              : bond        0.00578 (    3)
  SS BOND              : angle       1.56557 (    6)
  covalent geometry    : bond        0.00285 ( 7617)
  covalent geometry    : angle       0.61562 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 272
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7761 (mp10)
REVERT: B  124 TYR cc_start: 0.8003 (m-80) cc_final: 0.7543 (m-80)
REVERT: B  205 ASP cc_start: 0.8266 (p0) cc_final: 0.8060 (p0)
REVERT: B  280 LYS cc_start: 0.7518 (tttt) cc_final: 0.7255 (ttmt)
REVERT: N    3 GLN cc_start: 0.6907 (tt0) cc_final: 0.6675 (tm-30)
REVERT: N   34 MET cc_start: 0.8044 (mmm) cc_final: 0.7747 (mmt)
REVERT: N   60 TYR cc_start: 0.7714 (m-80) cc_final: 0.7501 (m-80)
REVERT: N  115 TYR cc_start: 0.7853 (t80) cc_final: 0.7297 (t80)
REVERT: R  137 TYR cc_start: 0.8730 (t80) cc_final: 0.7782 (t80)
REVERT: R  153 ILE cc_start: 0.8707 (mt) cc_final: 0.8479 (mt)
REVERT: R  170 LYS cc_start: 0.7371 (mttm) cc_final: 0.7167 (mttp)
REVERT: R  198 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6570 (mpt)
  outliers start: 29
  outliers final: 23
  residues processed: 283
  average time/residue: 0.1925
  time to fit residues: 72.0487
Evaluate side-chains
  291 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 266
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 92 optimal weight:    0.4980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.161702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.135651 restraints weight = 12635.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139888 restraints weight = 6908.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.142769 restraints weight = 4456.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7620  Z= 0.146
  Angle     :  0.638  12.638  10386  Z= 0.333
  Chirality :  0.044   0.186   1199
  Planarity :  0.004   0.051   1341
  Dihedral  :  4.532  17.087   1100
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 25.94 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.27), residues: 1013
  helix:  2.35 (0.26), residues: 402
  sheet: -0.06 (0.35), residues: 215
  loop : -1.87 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.022   0.002   PHE N 103 
 TYR   0.020   0.001   TYR A  37 
 ARG   0.006   0.000   ARG A 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  402)
  hydrogen bonds       : angle       4.55515 ( 1167)
  SS BOND              : bond        0.00622 (    3)
  SS BOND              : angle       1.61257 (    6)
  covalent geometry    : bond        0.00338 ( 7617)
  covalent geometry    : angle       0.63689 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 268
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7766 (mp10)
REVERT: B  124 TYR cc_start: 0.8043 (m-80) cc_final: 0.7590 (m-80)
REVERT: B  205 ASP cc_start: 0.8271 (p0) cc_final: 0.8068 (p0)
REVERT: B  280 LYS cc_start: 0.7572 (tttt) cc_final: 0.7297 (ttmt)
REVERT: B  301 LYS cc_start: 0.7312 (mptt) cc_final: 0.6860 (mttt)
REVERT: N    3 GLN cc_start: 0.6902 (tt0) cc_final: 0.6636 (tm-30)
REVERT: N   34 MET cc_start: 0.8035 (mmm) cc_final: 0.7750 (mmt)
REVERT: N   60 TYR cc_start: 0.7772 (m-80) cc_final: 0.7548 (m-10)
REVERT: N  115 TYR cc_start: 0.7887 (t80) cc_final: 0.7350 (t80)
REVERT: R  137 TYR cc_start: 0.8766 (t80) cc_final: 0.7795 (t80)
REVERT: R  153 ILE cc_start: 0.8743 (mt) cc_final: 0.8516 (mt)
REVERT: R  170 LYS cc_start: 0.7419 (mttm) cc_final: 0.7199 (mttp)
REVERT: R  198 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6628 (mpt)
REVERT: R  211 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7179 (t80)
  outliers start: 32
  outliers final: 26
  residues processed: 278
  average time/residue: 0.1938
  time to fit residues: 71.4330
Evaluate side-chains
  293 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 264
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  117 MET
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  211 TYR
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain R residue  275 GLU
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0060
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
A 284 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.164907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.139012 restraints weight = 12410.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.143338 restraints weight = 6768.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.146299 restraints weight = 4349.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7620  Z= 0.123
  Angle     :  0.637  12.623  10386  Z= 0.328
  Chirality :  0.044   0.189   1199
  Planarity :  0.004   0.052   1341
  Dihedral  :  4.330  17.040   1100
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 27.10 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.27), residues: 1013
  helix:  2.50 (0.26), residues: 398
  sheet:  0.01 (0.35), residues: 215
  loop : -1.80 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.020   0.001   PHE B 199 
 TYR   0.019   0.001   TYR A  37 
 ARG   0.003   0.000   ARG A  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03428 (  402)
  hydrogen bonds       : angle       4.40320 ( 1167)
  SS BOND              : bond        0.00564 (    3)
  SS BOND              : angle       1.48414 (    6)
  covalent geometry    : bond        0.00283 ( 7617)
  covalent geometry    : angle       0.63572 (10380)

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 262
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7681 (mp10)
REVERT: B  124 TYR cc_start: 0.7972 (m-80) cc_final: 0.7506 (m-80)
REVERT: B  280 LYS cc_start: 0.7531 (tttt) cc_final: 0.7257 (ttmt)
REVERT: B  301 LYS cc_start: 0.7172 (mptt) cc_final: 0.6813 (mttm)
REVERT: N    3 GLN cc_start: 0.6918 (tt0) cc_final: 0.6633 (tm-30)
REVERT: N   34 MET cc_start: 0.7925 (mmm) cc_final: 0.7650 (mmt)
REVERT: N   60 TYR cc_start: 0.7839 (m-80) cc_final: 0.7621 (m-10)
REVERT: N  115 TYR cc_start: 0.7806 (t80) cc_final: 0.7254 (t80)
REVERT: R  137 TYR cc_start: 0.8705 (t80) cc_final: 0.7718 (t80)
REVERT: R  198 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6402 (mpt)
REVERT: R  211 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6946 (t80)
REVERT: A  283 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7979 (mtmt)
  outliers start: 27
  outliers final: 21
  residues processed: 270
  average time/residue: 0.2023
  time to fit residues: 71.7833
Evaluate side-chains
  281 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 257
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  105 PHE
Chi-restraints excluded: chain R residue  120 LEU
Chi-restraints excluded: chain R residue  139 THR
Chi-restraints excluded: chain R residue  166 PHE
Chi-restraints excluded: chain R residue  197 MET
Chi-restraints excluded: chain R residue  198 MET
Chi-restraints excluded: chain R residue  205 LEU
Chi-restraints excluded: chain R residue  211 TYR
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  282 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 35 optimal weight:    0.4980
   chunk 34 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    0.2980
   chunk 64 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
N 123 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.159818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.134395 restraints weight = 12551.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138500 restraints weight = 6917.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.141310 restraints weight = 4480.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7620  Z= 0.189
  Angle     :  0.683  12.432  10386  Z= 0.356
  Chirality :  0.046   0.197   1199
  Planarity :  0.004   0.050   1341
  Dihedral  :  4.607  17.320   1100
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 27.25 %
    Favored  : 68.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.27), residues: 1013
  helix:  2.21 (0.26), residues: 406
  sheet:  0.04 (0.36), residues: 215
  loop : -1.84 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.021   0.002   PHE B 199 
 TYR   0.021   0.002   TYR A  37 
 ARG   0.002   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  402)
  hydrogen bonds       : angle       4.61282 ( 1167)
  SS BOND              : bond        0.00851 (    3)
  SS BOND              : angle       1.86614 (    6)
  covalent geometry    : bond        0.00430 ( 7617)
  covalent geometry    : angle       0.68205 (10380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3318.61 seconds
wall clock time: 58 minutes 29.76 seconds (3509.76 seconds total)