Starting phenix.real_space_refine
on Fri Aug 22 19:44:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hj2_33481/08_2025/8hj2_33481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hj2_33481/08_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_33481/08_2025/8hj2_33481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hj2_33481/08_2025/8hj2_33481.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hj2_33481/08_2025/8hj2_33481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hj2_33481/08_2025/8hj2_33481.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 8, 'GLN:plan1': 5, 'GLU:plan': 2, '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: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1}
          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: {'ASN:plan1': 6, 'PHE:plan': 11, 'HIS:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 5, 'TRP:plan': 1, 'TYR:plan': 1}
          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: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 55
  Time building chain proxies: 1.84, per 1000 atoms: 0.25
  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: 0.54
  Conformation dependent library (CDL) restraints added in 322.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.27
  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: 1.15

  Time building geometry restraints manager: 0.71 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:             1.120
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.390
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.710
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.023   0.002   ARG B  68 
 TYR   0.054   0.004   TYR A 350 
 PHE   0.044   0.004   PHE N  29 
 TRP   0.058   0.005   TRP B 169 
 HIS   0.010   0.003   HIS A 347 

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

*********************** 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  : 0.179 
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: 0.0886
  time to fit residues: 35.6541
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  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.160057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133559 restraints weight = 12534.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.137778 restraints weight = 6944.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.140525 restraints weight = 4535.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.142712 restraints weight = 3344.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144085 restraints weight = 2642.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7620  Z= 0.164
  Angle     :  0.665   8.306  10386  Z= 0.355
  Chirality :  0.045   0.174   1199
  Planarity :  0.005   0.067   1341
  Dihedral  :  5.705  20.487   1100
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.20 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.25), residues: 1013
  helix:  0.71 (0.25), residues: 409
  sheet: -0.41 (0.35), residues: 217
  loop : -2.05 (0.27), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N  19 
 TYR   0.017   0.001   TYR A 350 
 PHE   0.020   0.002   PHE R 272 
 TRP   0.029   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7617)
  covalent geometry    : angle       0.66140 (10380)
  SS BOND              : bond        0.00983 (    3)
  SS BOND              : angle       2.89560 (    6)
  hydrogen bonds       : bond        0.04857 (  402)
  hydrogen bonds       : angle       5.35516 ( 1167)

*********************** 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
  314 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 291
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7100 (mmt)
REVERT: N   34 MET cc_start: 0.7719 (mmm) cc_final: 0.7375 (mmt)
REVERT: N   60 TYR cc_start: 0.7665 (m-80) cc_final: 0.7046 (m-80)
REVERT: N   67 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6472 (ttp80)
REVERT: R   67 PHE cc_start: 0.8590 (m-80) cc_final: 0.8349 (m-80)
REVERT: R  137 TYR cc_start: 0.8736 (t80) cc_final: 0.8015 (t80)
REVERT: A  209 GLU cc_start: 0.6981 (pp20) cc_final: 0.6666 (pp20)
REVERT: A  220 HIS cc_start: 0.8088 (t70) cc_final: 0.7424 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 297
  average time/residue: 0.0783
  time to fit residues: 30.9967
Evaluate side-chains
  300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 283
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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 8 optimal weight:    1.9990
   chunk 49 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 78 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 62 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
R 221 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.159091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133704 restraints weight = 12315.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.137675 restraints weight = 6759.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.140482 restraints weight = 4415.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.142244 restraints weight = 3208.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.143754 restraints weight = 2571.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2063

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= 0.153
  Angle     :  0.613   7.918  10386  Z= 0.329
  Chirality :  0.044   0.167   1199
  Planarity :  0.004   0.045   1341
  Dihedral  :  5.141  17.797   1100
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.54 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.26), residues: 1013
  helix:  1.57 (0.26), residues: 402
  sheet: -0.32 (0.35), residues: 215
  loop : -1.90 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  19 
 TYR   0.011   0.001   TYR A 350 
 PHE   0.023   0.002   PHE A 366 
 TRP   0.021   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7617)
  covalent geometry    : angle       0.61087 (10380)
  SS BOND              : bond        0.00821 (    3)
  SS BOND              : angle       2.33361 (    6)
  hydrogen bonds       : bond        0.04259 (  402)
  hydrogen bonds       : angle       4.88972 ( 1167)

*********************** 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
  319 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 289
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.7950 (m-80) cc_final: 0.7596 (m-80)
REVERT: B  205 ASP cc_start: 0.8396 (p0) cc_final: 0.8193 (p0)
REVERT: B  241 PHE cc_start: 0.8612 (p90) cc_final: 0.8314 (p90)
REVERT: B  261 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8011 (mm)
REVERT: N    3 GLN cc_start: 0.6856 (tt0) cc_final: 0.6587 (tm-30)
REVERT: N   34 MET cc_start: 0.7885 (mmm) cc_final: 0.7585 (mmt)
REVERT: N   60 TYR cc_start: 0.7737 (m-80) cc_final: 0.7375 (m-80)
REVERT: N   67 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6808 (ttp80)
REVERT: N   87 LYS cc_start: 0.8010 (tttt) cc_final: 0.7452 (tttt)
REVERT: N  115 TYR cc_start: 0.7735 (t80) cc_final: 0.7535 (t80)
REVERT: R  126 ASP cc_start: 0.8833 (t0) cc_final: 0.8617 (t0)
REVERT: R  137 TYR cc_start: 0.8760 (t80) cc_final: 0.8045 (t80)
REVERT: R  217 ILE cc_start: 0.8686 (mm) cc_final: 0.8451 (mt)
REVERT: R  275 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6977 (tt0)
REVERT: A  209 GLU cc_start: 0.7028 (pp20) cc_final: 0.6536 (pp20)
REVERT: A  220 HIS cc_start: 0.8029 (t70) cc_final: 0.7223 (t70)
  outliers start: 30
  outliers final: 18
  residues processed: 297
  average time/residue: 0.0795
  time to fit residues: 31.4910
Evaluate side-chains
  300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 280
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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  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  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 54 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.161417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.135431 restraints weight = 12471.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139732 restraints weight = 6802.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.142636 restraints weight = 4356.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.144526 restraints weight = 3154.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145989 restraints weight = 2512.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7620  Z= 0.127
  Angle     :  0.593   7.600  10386  Z= 0.316
  Chirality :  0.043   0.159   1199
  Planarity :  0.004   0.046   1341
  Dihedral  :  4.810  16.836   1100
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 20.00 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.27), residues: 1013
  helix:  1.98 (0.26), residues: 404
  sheet: -0.18 (0.35), residues: 215
  loop : -1.76 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.020   0.001   TYR R 211 
 PHE   0.023   0.002   PHE R 107 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7617)
  covalent geometry    : angle       0.59122 (10380)
  SS BOND              : bond        0.00681 (    3)
  SS BOND              : angle       1.98362 (    6)
  hydrogen bonds       : bond        0.03865 (  402)
  hydrogen bonds       : angle       4.65452 ( 1167)

*********************** 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
  310 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 278
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.7940 (m-80) cc_final: 0.7599 (m-80)
REVERT: B  154 ASP cc_start: 0.8249 (t0) cc_final: 0.7916 (t0)
REVERT: B  205 ASP cc_start: 0.8370 (p0) cc_final: 0.8140 (p0)
REVERT: B  241 PHE cc_start: 0.8577 (p90) cc_final: 0.8325 (p90)
REVERT: B  251 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7480 (mtm-85)
REVERT: B  280 LYS cc_start: 0.7526 (tttt) cc_final: 0.7281 (ttmt)
REVERT: N    3 GLN cc_start: 0.6819 (tt0) cc_final: 0.6603 (tm-30)
REVERT: N   34 MET cc_start: 0.7890 (mmm) cc_final: 0.7478 (mmt)
REVERT: N   60 TYR cc_start: 0.7759 (m-80) cc_final: 0.7443 (m-80)
REVERT: N   67 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6594 (ttp80)
REVERT: N   89 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6853 (mm-30)
REVERT: N  115 TYR cc_start: 0.7736 (t80) cc_final: 0.7401 (t80)
REVERT: R  137 TYR cc_start: 0.8738 (t80) cc_final: 0.7925 (t80)
REVERT: R  211 TYR cc_start: 0.7675 (m-80) cc_final: 0.7450 (t80)
REVERT: R  217 ILE cc_start: 0.8720 (mm) cc_final: 0.8487 (mt)
REVERT: R  275 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6930 (tt0)
REVERT: A  209 GLU cc_start: 0.6919 (pp20) cc_final: 0.6698 (pp20)
REVERT: A  211 LYS cc_start: 0.7167 (mmtp) cc_final: 0.6699 (mmtm)
REVERT: A  220 HIS cc_start: 0.7896 (t70) cc_final: 0.7212 (t70)
REVERT: A  263 PHE cc_start: 0.9173 (t80) cc_final: 0.8950 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 291
  average time/residue: 0.0815
  time to fit residues: 31.5981
Evaluate side-chains
  292 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 270
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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   89 LYS
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  284 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   67 ARG
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  205 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  274 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 90 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 2 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.159320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.133784 restraints weight = 12468.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.137899 restraints weight = 6839.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.140676 restraints weight = 4416.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.142557 restraints weight = 3212.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.143972 restraints weight = 2555.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7620  Z= 0.159
  Angle     :  0.630  12.866  10386  Z= 0.333
  Chirality :  0.044   0.155   1199
  Planarity :  0.004   0.047   1341
  Dihedral  :  4.772  18.074   1100
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.59 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.27), residues: 1013
  helix:  2.10 (0.26), residues: 399
  sheet: -0.14 (0.35), residues: 216
  loop : -1.81 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  19 
 TYR   0.019   0.002   TYR A  37 
 PHE   0.027   0.002   PHE R 107 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7617)
  covalent geometry    : angle       0.62812 (10380)
  SS BOND              : bond        0.00768 (    3)
  SS BOND              : angle       1.92082 (    6)
  hydrogen bonds       : bond        0.03995 (  402)
  hydrogen bonds       : angle       4.70559 ( 1167)

*********************** 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
  310 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 276
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.8049 (m-80) cc_final: 0.7664 (m-80)
REVERT: B  205 ASP cc_start: 0.8322 (p0) cc_final: 0.8085 (p0)
REVERT: B  241 PHE cc_start: 0.8621 (p90) cc_final: 0.8360 (p90)
REVERT: B  280 LYS cc_start: 0.7500 (tttt) cc_final: 0.7227 (ttmt)
REVERT: N    3 GLN cc_start: 0.6815 (tt0) cc_final: 0.6597 (tm-30)
REVERT: N   34 MET cc_start: 0.7933 (mmm) cc_final: 0.7584 (mmt)
REVERT: N   60 TYR cc_start: 0.7731 (m-80) cc_final: 0.7465 (m-80)
REVERT: N   67 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6599 (ttp80)
REVERT: N   87 LYS cc_start: 0.8086 (tttt) cc_final: 0.7834 (tttt)
REVERT: N  115 TYR cc_start: 0.7790 (t80) cc_final: 0.7453 (t80)
REVERT: R  126 ASP cc_start: 0.8836 (t0) cc_final: 0.8592 (t0)
REVERT: R  137 TYR cc_start: 0.8760 (t80) cc_final: 0.7984 (t80)
REVERT: R  198 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6739 (mpt)
REVERT: R  217 ILE cc_start: 0.8718 (mm) cc_final: 0.8447 (mt)
REVERT: A  209 GLU cc_start: 0.7031 (pp20) cc_final: 0.6726 (pp20)
REVERT: A  220 HIS cc_start: 0.8046 (t70) cc_final: 0.7383 (t70)
  outliers start: 34
  outliers final: 27
  residues processed: 291
  average time/residue: 0.0727
  time to fit residues: 28.4567
Evaluate side-chains
  299 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 270
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  331 SER
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   63 THR
Chi-restraints excluded: chain R residue  105 PHE
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  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 A residue   45 LEU
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 83 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 352 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 = 0.3932 r_free = 0.3932 target = 0.155030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.129608 restraints weight = 12721.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.133496 restraints weight = 7020.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.136323 restraints weight = 4600.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138118 restraints weight = 3362.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.139478 restraints weight = 2699.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   7620  Z= 0.234
  Angle     :  0.684   9.374  10386  Z= 0.368
  Chirality :  0.046   0.153   1199
  Planarity :  0.005   0.046   1341
  Dihedral  :  5.073  17.716   1100
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.74 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1013
  helix:  1.73 (0.26), residues: 409
  sheet: -0.15 (0.35), residues: 216
  loop : -1.96 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG N  19 
 TYR   0.019   0.002   TYR B 105 
 PHE   0.022   0.002   PHE A 366 
 TRP   0.020   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 7617)
  covalent geometry    : angle       0.68192 (10380)
  SS BOND              : bond        0.01052 (    3)
  SS BOND              : angle       2.41396 (    6)
  hydrogen bonds       : bond        0.04586 (  402)
  hydrogen bonds       : angle       4.98509 ( 1167)

*********************** 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
  307 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 270
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.8054 (m-80) cc_final: 0.7707 (m-80)
REVERT: B  205 ASP cc_start: 0.8455 (p0) cc_final: 0.8200 (p0)
REVERT: B  241 PHE cc_start: 0.8728 (p90) cc_final: 0.8446 (p90)
REVERT: N    3 GLN cc_start: 0.6911 (tt0) cc_final: 0.6679 (tm-30)
REVERT: N   34 MET cc_start: 0.8041 (mmm) cc_final: 0.7691 (mmt)
REVERT: N   60 TYR cc_start: 0.7655 (m-80) cc_final: 0.7432 (m-80)
REVERT: N   87 LYS cc_start: 0.7988 (tttt) cc_final: 0.7740 (tttt)
REVERT: N  115 TYR cc_start: 0.7914 (t80) cc_final: 0.7543 (t80)
REVERT: R  126 ASP cc_start: 0.8896 (t0) cc_final: 0.8680 (t0)
REVERT: R  137 TYR cc_start: 0.8822 (t80) cc_final: 0.8040 (t80)
REVERT: R  198 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.6917 (mpt)
REVERT: R  211 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7329 (t80)
REVERT: R  217 ILE cc_start: 0.8703 (mm) cc_final: 0.8434 (mt)
REVERT: R  275 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6908 (tt0)
  outliers start: 37
  outliers final: 27
  residues processed: 283
  average time/residue: 0.0794
  time to fit residues: 29.8425
Evaluate side-chains
  294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 265
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  164 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  336 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  166 PHE
Chi-restraints excluded: chain R residue  177 VAL
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   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  282 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.9186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.160100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.134698 restraints weight = 12501.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.138890 restraints weight = 6770.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.141765 restraints weight = 4350.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.143739 restraints weight = 3143.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.144899 restraints weight = 2472.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7620  Z= 0.138
  Angle     :  0.619   8.505  10386  Z= 0.326
  Chirality :  0.044   0.160   1199
  Planarity :  0.004   0.048   1341
  Dihedral  :  4.708  16.663   1100
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 24.35 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.27), residues: 1013
  helix:  2.09 (0.26), residues: 405
  sheet: -0.14 (0.35), residues: 214
  loop : -1.90 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  19 
 TYR   0.019   0.001   TYR R 211 
 PHE   0.024   0.002   PHE A 366 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7617)
  covalent geometry    : angle       0.61748 (10380)
  SS BOND              : bond        0.00792 (    3)
  SS BOND              : angle       1.90287 (    6)
  hydrogen bonds       : bond        0.03899 (  402)
  hydrogen bonds       : angle       4.65981 ( 1167)

*********************** 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
  303 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 274
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 TYR cc_start: 0.8084 (m-80) cc_final: 0.7621 (m-80)
REVERT: B  205 ASP cc_start: 0.8323 (p0) cc_final: 0.8084 (p0)
REVERT: B  241 PHE cc_start: 0.8667 (p90) cc_final: 0.8389 (p90)
REVERT: B  280 LYS cc_start: 0.7525 (tttt) cc_final: 0.7252 (ttmt)
REVERT: N   34 MET cc_start: 0.8013 (mmm) cc_final: 0.7682 (mmt)
REVERT: N   60 TYR cc_start: 0.7699 (m-80) cc_final: 0.7492 (m-80)
REVERT: N  115 TYR cc_start: 0.7847 (t80) cc_final: 0.7379 (t80)
REVERT: R  137 TYR cc_start: 0.8769 (t80) cc_final: 0.7865 (t80)
REVERT: R  198 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6638 (mpt)
REVERT: R  211 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: R  275 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6928 (tt0)
  outliers start: 29
  outliers final: 24
  residues processed: 282
  average time/residue: 0.0841
  time to fit residues: 31.7529
Evaluate side-chains
  297 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 271
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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   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 R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue   68 ILE
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 A residue   54 SER
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 49 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 99 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.161188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.135551 restraints weight = 12475.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.139830 restraints weight = 6725.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142589 restraints weight = 4294.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.144708 restraints weight = 3124.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.145975 restraints weight = 2450.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7620  Z= 0.134
  Angle     :  0.637  13.942  10386  Z= 0.329
  Chirality :  0.044   0.169   1199
  Planarity :  0.004   0.049   1341
  Dihedral  :  4.586  17.066   1100
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 24.20 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.27), residues: 1013
  helix:  2.31 (0.27), residues: 398
  sheet: -0.11 (0.35), residues: 218
  loop : -1.83 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  68 
 TYR   0.019   0.001   TYR A  37 
 PHE   0.021   0.002   PHE A 222 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7617)
  covalent geometry    : angle       0.63539 (10380)
  SS BOND              : bond        0.00756 (    3)
  SS BOND              : angle       1.79285 (    6)
  hydrogen bonds       : bond        0.03730 (  402)
  hydrogen bonds       : angle       4.57118 ( 1167)

*********************** 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
  300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 268
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7765 (mp10)
REVERT: B  124 TYR cc_start: 0.8022 (m-80) cc_final: 0.7523 (m-80)
REVERT: B  205 ASP cc_start: 0.8308 (p0) cc_final: 0.8072 (p0)
REVERT: B  241 PHE cc_start: 0.8648 (p90) cc_final: 0.8373 (p90)
REVERT: B  280 LYS cc_start: 0.7539 (tttt) cc_final: 0.7266 (ttmt)
REVERT: N   34 MET cc_start: 0.7995 (mmm) cc_final: 0.7717 (mmt)
REVERT: N   60 TYR cc_start: 0.7755 (m-80) cc_final: 0.7548 (m-80)
REVERT: N  115 TYR cc_start: 0.7815 (t80) cc_final: 0.7380 (t80)
REVERT: R  198 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6574 (mpt)
REVERT: R  211 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7022 (t80)
REVERT: R  275 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6929 (tt0)
REVERT: A  220 HIS cc_start: 0.8152 (t70) cc_final: 0.7849 (t70)
  outliers start: 32
  outliers final: 27
  residues processed: 277
  average time/residue: 0.0841
  time to fit residues: 31.0236
Evaluate side-chains
  293 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 263
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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   20 LEU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue   68 ILE
Chi-restraints excluded: chain R residue  105 PHE
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  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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0050
   chunk 33 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   overall best weight:    2.1598

-------------------------------------------------------------------------------
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 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 = 0.3955 r_free = 0.3955 target = 0.157027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131849 restraints weight = 12659.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.135873 restraints weight = 6920.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138644 restraints weight = 4467.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.140445 restraints weight = 3237.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.141436 restraints weight = 2583.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   7620  Z= 0.223
  Angle     :  0.694  10.128  10386  Z= 0.369
  Chirality :  0.046   0.211   1199
  Planarity :  0.005   0.085   1341
  Dihedral  :  4.968  19.277   1100
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.06 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.27), residues: 1013
  helix:  1.97 (0.26), residues: 402
  sheet: -0.02 (0.36), residues: 216
  loop : -1.94 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  68 
 TYR   0.020   0.002   TYR A  37 
 PHE   0.022   0.002   PHE A 366 
 TRP   0.021   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 7617)
  covalent geometry    : angle       0.69226 (10380)
  SS BOND              : bond        0.01061 (    3)
  SS BOND              : angle       2.30404 (    6)
  hydrogen bonds       : bond        0.04353 (  402)
  hydrogen bonds       : angle       4.89761 ( 1167)

*********************** 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
  302 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 267
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7824 (mp10)
REVERT: B  124 TYR cc_start: 0.8092 (m-80) cc_final: 0.7659 (m-80)
REVERT: B  205 ASP cc_start: 0.8366 (p0) cc_final: 0.8146 (p0)
REVERT: B  241 PHE cc_start: 0.8775 (p90) cc_final: 0.8486 (p90)
REVERT: B  251 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7611 (mtm-85)
REVERT: B  280 LYS cc_start: 0.7562 (tttt) cc_final: 0.7264 (ttmt)
REVERT: N   34 MET cc_start: 0.8110 (mmm) cc_final: 0.7832 (mmt)
REVERT: N  115 TYR cc_start: 0.7881 (t80) cc_final: 0.7452 (t80)
REVERT: R  198 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6817 (mpt)
REVERT: R  211 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7175 (t80)
REVERT: R  217 ILE cc_start: 0.8774 (mm) cc_final: 0.8487 (mt)
REVERT: R  275 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6851 (tt0)
REVERT: A  211 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7337 (mmtp)
  outliers start: 35
  outliers final: 27
  residues processed: 278
  average time/residue: 0.0904
  time to fit residues: 33.3252
Evaluate side-chains
  295 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  318 LEU
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   68 ILE
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  211 TYR
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  211 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 1 optimal weight:   40.0000
   chunk 45 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0870
   chunk 84 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 47 optimal weight:    0.3980
   chunk 23 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 220 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 = 0.4022 r_free = 0.4022 target = 0.163464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.137680 restraints weight = 12342.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.141911 restraints weight = 6731.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.144802 restraints weight = 4334.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.146812 restraints weight = 3142.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.147961 restraints weight = 2482.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7620  Z= 0.127
  Angle     :  0.647   9.052  10386  Z= 0.337
  Chirality :  0.044   0.183   1199
  Planarity :  0.004   0.050   1341
  Dihedral  :  4.568  21.085   1100
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 26.38 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.27), residues: 1013
  helix:  2.27 (0.27), residues: 398
  sheet: -0.02 (0.36), residues: 213
  loop : -1.76 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 147 
 TYR   0.018   0.001   TYR R 211 
 PHE   0.024   0.001   PHE A 366 
 TRP   0.017   0.002   TRP B 297 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7617)
  covalent geometry    : angle       0.64619 (10380)
  SS BOND              : bond        0.00713 (    3)
  SS BOND              : angle       1.69434 (    6)
  hydrogen bonds       : bond        0.03705 (  402)
  hydrogen bonds       : angle       4.58961 ( 1167)

********************** 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
  294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 270
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7595 (mtp-110)
REVERT: B  124 TYR cc_start: 0.7914 (m-80) cc_final: 0.7452 (m-80)
REVERT: B  205 ASP cc_start: 0.8255 (p0) cc_final: 0.8006 (p0)
REVERT: B  241 PHE cc_start: 0.8620 (p90) cc_final: 0.8376 (p90)
REVERT: B  280 LYS cc_start: 0.7539 (tttt) cc_final: 0.7265 (ttmt)
REVERT: N  115 TYR cc_start: 0.7821 (t80) cc_final: 0.7370 (t80)
REVERT: R  137 TYR cc_start: 0.8698 (t80) cc_final: 0.7758 (t80)
REVERT: R  198 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6439 (mpt)
REVERT: R  211 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7033 (t80)
REVERT: R  275 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6773 (tt0)
  outliers start: 24
  outliers final: 17
  residues processed: 280
  average time/residue: 0.0909
  time to fit residues: 33.9640
Evaluate side-chains
  283 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 264
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
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   20 LEU
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue   63 THR
Chi-restraints excluded: chain R residue   68 ILE
Chi-restraints excluded: chain R residue  120 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  211 TYR
Chi-restraints excluded: chain R residue  215 PHE
Chi-restraints excluded: chain A residue  224 VAL
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 82 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0170
   chunk 70 optimal weight:    0.2980
   chunk 97 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    1.0624

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
N   5 GLN
** A 220 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 = 0.4000 r_free = 0.4000 target = 0.161567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.136311 restraints weight = 12196.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.140516 restraints weight = 6584.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.143357 restraints weight = 4221.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.145196 restraints weight = 3044.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.146693 restraints weight = 2417.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7620  Z= 0.149
  Angle     :  0.656   8.905  10386  Z= 0.345
  Chirality :  0.045   0.184   1199
  Planarity :  0.005   0.084   1341
  Dihedral  :  4.620  20.279   1100
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 27.54 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.27), residues: 1013
  helix:  2.21 (0.27), residues: 402
  sheet:  0.06 (0.36), residues: 218
  loop : -1.76 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG R 147 
 TYR   0.018   0.001   TYR A  37 
 PHE   0.022   0.002   PHE A 366 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7617)
  covalent geometry    : angle       0.65514 (10380)
  SS BOND              : bond        0.00707 (    3)
  SS BOND              : angle       1.66195 (    6)
  hydrogen bonds       : bond        0.03791 (  402)
  hydrogen bonds       : angle       4.63079 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1412.42 seconds
wall clock time: 25 minutes 2.37 seconds (1502.37 seconds total)