Starting phenix.real_space_refine
on Tue Mar 11 20:38:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge4_29955/03_2025/8ge4_29955.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.036
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      45      5.16       5
     C    4285      2.51       5
     N    1140      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6646
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1746
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 174
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 141
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 123
    Chain: "B"
      Number of atoms: 2359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2359
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 141
    Chain: "G"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 344
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "R"
      Number of atoms: 2181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2181
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 75
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 4.65, per 1000 atoms: 0.70
  Number of scatterers: 6646
  At special positions: 0
  Unit cell: (68.9, 97.52, 127.2, 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      45     16.00
     O    1176      8.00
     N    1140      7.00
     C    4285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 933.6 milliseconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      48.6% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.378A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.786A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.689A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.775A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.554A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.547A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.546A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.561A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.842A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.468A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.609A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.185A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.645A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 4.063A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 341
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.462A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.721A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.555A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.727A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.638A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.884A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.548A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.843A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1125 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: 1.90

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2136
        1.34 -     1.46: 1611
        1.46 -     1.58: 2983
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.82e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.85e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.437 -0.043 2.00e-02 2.50e+03 4.63e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.60e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.323  0.030 2.00e-02 2.50e+03 2.31e+00
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 9035
        1.15 -     2.30: 187
        2.30 -     3.45: 39
        3.45 -     4.59: 4
        4.59 -     5.74: 11
  Bond angle restraints: 9276
  Sorted by residual:
  angle pdb=" N   GLY A 329 "
        pdb=" CA  GLY A 329 "
        pdb=" C   GLY A 329 "
      ideal   model   delta    sigma   weight residual
     113.18  107.44    5.74 2.37e+00 1.78e-01 5.87e+00
  angle pdb=" CA  GLU A  50 "
        pdb=" CB  GLU A  50 "
        pdb=" CG  GLU A  50 "
      ideal   model   delta    sigma   weight residual
     114.10  118.52   -4.42 2.00e+00 2.50e-01 4.88e+00
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     122.46  125.55   -3.09 1.41e+00 5.03e-01 4.80e+00
  angle pdb=" C   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" CB  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     114.00  111.22    2.78 1.31e+00 5.83e-01 4.51e+00
  angle pdb=" C   TYR A 391 "
        pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
      ideal   model   delta    sigma   weight residual
     122.21  119.08    3.13 1.48e+00 4.57e-01 4.47e+00
  ... (remaining 9271 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 3585
       16.94 -    33.88: 301
       33.88 -    50.81: 42
       50.81 -    67.75: 5
       67.75 -    84.69: 2
  Dihedral angle restraints: 3935
    sinusoidal: 1308
      harmonic: 2627
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.69   18.31     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  ASP B  76 "
           pdb=" C   ASP B  76 "
           pdb=" N   GLY B  77 "
           pdb=" CA  GLY B  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.88  -17.12     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASP B 333 "
           pdb=" C   ASP B 333 "
           pdb=" N   SER B 334 "
           pdb=" CA  SER B 334 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.35  -15.65     0      5.00e+00 4.00e-02 9.79e+00
  ... (remaining 3932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 731
       0.030 -    0.060: 242
       0.060 -    0.091: 88
       0.091 -    0.121: 40
       0.121 -    0.151: 3
  Chirality restraints: 1104
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 1101 not shown)

  Planarity restraints: 1164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  38 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO B  39 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B  39 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  39 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.009 2.00e-02 2.50e+03   8.45e-03 1.43e+00
        pdb=" CG  TYR B  59 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  50 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   GLU A  50 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLU A  50 "    0.008 2.00e-02 2.50e+03
        pdb=" N   SER A  51 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1161 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1426
        2.78 -     3.31: 6329
        3.31 -     3.84: 11129
        3.84 -     4.37: 12527
        4.37 -     4.90: 22886
  Nonbonded interactions: 54297
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 392 "
            pdb=" OG1 THR R 274 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" NE2 GLN B  75 "
            pdb=" O   VAL B 100 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OE1 GLN A  19 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" NE2 HIS B 311 "
            pdb=" OG1 THR B 329 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.341 3.040
  ... (remaining 54292 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.470
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
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      :  0.003   0.052   6792  Z= 0.200
  Angle     :  0.453   5.742   9276  Z= 0.242
  Chirality :  0.038   0.151   1104
  Planarity :  0.003   0.031   1164
  Dihedral  : 12.450  84.690   2226
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.29), residues: 885
  helix:  2.49 (0.26), residues: 404
  sheet:  0.01 (0.40), residues: 168
  loop : -0.12 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  82 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.002   0.000   ARG R 239 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8400 (t0) cc_final: 0.8032 (t0)
REVERT: A  339 TYR cc_start: 0.8312 (m-80) cc_final: 0.7722 (m-80)
REVERT: B  274 THR cc_start: 0.9326 (m) cc_final: 0.9033 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2012
  time to fit residues: 33.5020
Evaluate side-chains
  100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 239 ASN
B 266 HIS
R 178 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116539 restraints weight = 9976.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.08
r_work: 0.3345 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6792  Z= 0.214
  Angle     :  0.490   6.644   9276  Z= 0.265
  Chirality :  0.040   0.143   1104
  Planarity :  0.003   0.026   1164
  Dihedral  :  4.729  70.074    972
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  8.41 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.30), residues: 885
  helix:  2.41 (0.26), residues: 408
  sheet: -0.07 (0.39), residues: 170
  loop :  0.06 (0.39), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 339 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 239 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8572 (t0) cc_final: 0.8223 (t0)
REVERT: A  339 TYR cc_start: 0.8686 (m-80) cc_final: 0.7987 (m-80)
REVERT: B  274 THR cc_start: 0.9337 (m) cc_final: 0.9029 (p)
REVERT: R  185 TYR cc_start: 0.6946 (m-10) cc_final: 0.6744 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1970
  time to fit residues: 30.6296
Evaluate side-chains
  106 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    0.0050
   chunk 74 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0070
   chunk 24 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.4412

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.136302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.118038 restraints weight = 10102.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.09
r_work: 0.3365 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6792  Z= 0.146
  Angle     :  0.450   5.589   9276  Z= 0.241
  Chirality :  0.039   0.136   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.629  70.161    972
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.11 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.29), residues: 885
  helix:  2.52 (0.26), residues: 408
  sheet:  0.01 (0.39), residues: 170
  loop :  0.01 (0.38), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 256 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8560 (t0) cc_final: 0.8141 (t0)
REVERT: A  339 TYR cc_start: 0.8657 (m-80) cc_final: 0.7986 (m-80)
REVERT: B  274 THR cc_start: 0.9318 (m) cc_final: 0.9033 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 119
  average time/residue: 0.2062
  time to fit residues: 32.3843
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.134546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116234 restraints weight = 10215.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.09
r_work: 0.3340 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6792  Z= 0.198
  Angle     :  0.460   5.482   9276  Z= 0.247
  Chirality :  0.039   0.135   1104
  Planarity :  0.003   0.026   1164
  Dihedral  :  4.708  71.565    972
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.06 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.29), residues: 885
  helix:  2.50 (0.26), residues: 408
  sheet: -0.02 (0.39), residues: 173
  loop :  0.01 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 239 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8634 (t0) cc_final: 0.8244 (t0)
REVERT: A  339 TYR cc_start: 0.8684 (m-80) cc_final: 0.7953 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1855
  time to fit residues: 27.7084
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  164 THR
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0570
   chunk 7 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.118647 restraints weight = 9991.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.98
r_work: 0.3365 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6792  Z= 0.161
  Angle     :  0.441   5.352   9276  Z= 0.237
  Chirality :  0.039   0.133   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.613  71.780    972
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.17 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.29), residues: 885
  helix:  2.55 (0.26), residues: 412
  sheet: -0.13 (0.38), residues: 178
  loop :  0.07 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 228 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8632 (t0) cc_final: 0.8243 (t0)
REVERT: A  339 TYR cc_start: 0.8650 (m-80) cc_final: 0.7930 (m-80)
REVERT: B   43 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: B  301 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8818 (mttp)
  outliers start: 11
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1942
  time to fit residues: 29.2613
Evaluate side-chains
  108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 22 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.136795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.119299 restraints weight = 9936.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.97
r_work: 0.3373 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6792  Z= 0.150
  Angle     :  0.437   5.371   9276  Z= 0.235
  Chirality :  0.038   0.134   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.569  71.653    972
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.81 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.29), residues: 885
  helix:  2.62 (0.26), residues: 411
  sheet: -0.02 (0.38), residues: 176
  loop :  0.04 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 228 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8633 (t0) cc_final: 0.8246 (t0)
REVERT: A  339 TYR cc_start: 0.8613 (m-80) cc_final: 0.7890 (m-80)
REVERT: B   43 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8468 (mt)
REVERT: B  301 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8798 (mttp)
  outliers start: 15
  outliers final: 12
  residues processed: 112
  average time/residue: 0.1885
  time to fit residues: 28.1152
Evaluate side-chains
  108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0980
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.135033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116830 restraints weight = 10036.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.06
r_work: 0.3356 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6792  Z= 0.179
  Angle     :  0.449   5.339   9276  Z= 0.240
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.633  72.193    972
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.81 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.29), residues: 885
  helix:  2.60 (0.26), residues: 411
  sheet: -0.10 (0.38), residues: 179
  loop : -0.02 (0.38), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 228 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8660 (t0) cc_final: 0.8303 (t0)
REVERT: A  339 TYR cc_start: 0.8682 (m-80) cc_final: 0.7975 (m-80)
REVERT: B   43 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8498 (mt)
REVERT: B  301 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8791 (mttp)
  outliers start: 14
  outliers final: 12
  residues processed: 107
  average time/residue: 0.1952
  time to fit residues: 28.1001
Evaluate side-chains
  108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0470
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0570
   chunk 41 optimal weight:    0.2980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.3596

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.141967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123608 restraints weight = 9785.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.01
r_work: 0.3459 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6792  Z= 0.135
  Angle     :  0.429   5.364   9276  Z= 0.229
  Chirality :  0.038   0.134   1104
  Planarity :  0.003   0.028   1164
  Dihedral  :  4.512  71.644    972
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.81 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.29), residues: 885
  helix:  2.69 (0.26), residues: 411
  sheet: -0.16 (0.38), residues: 181
  loop :  0.00 (0.38), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 228 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8653 (t0) cc_final: 0.8269 (t0)
REVERT: A  339 TYR cc_start: 0.8648 (m-80) cc_final: 0.7988 (m-80)
REVERT: B   43 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: B  301 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8789 (mttm)
  outliers start: 15
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1867
  time to fit residues: 28.5105
Evaluate side-chains
  108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0010
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0470
   chunk 88 optimal weight:    0.4980
   chunk 37 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.2684

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.143069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.124641 restraints weight = 9813.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.02
r_work: 0.3478 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6792  Z= 0.126
  Angle     :  0.429   5.339   9276  Z= 0.229
  Chirality :  0.038   0.134   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.457  71.534    972
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.44 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.29), residues: 885
  helix:  2.72 (0.25), residues: 411
  sheet: -0.03 (0.38), residues: 179
  loop : -0.01 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.000   HIS B 183 
 PHE   0.007   0.001   PHE B 241 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 228 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8674 (t0) cc_final: 0.8272 (t0)
REVERT: A  339 TYR cc_start: 0.8636 (m-80) cc_final: 0.8070 (m-80)
REVERT: B   43 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8411 (mt)
REVERT: B  301 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8801 (mttm)
  outliers start: 15
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1801
  time to fit residues: 26.4763
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121695 restraints weight = 9931.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.03
r_work: 0.3432 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3342
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3342
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6792  Z= 0.185
  Angle     :  0.454   6.539   9276  Z= 0.241
  Chirality :  0.039   0.134   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.587  72.770    972
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.76 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.29), residues: 885
  helix:  2.70 (0.26), residues: 408
  sheet: -0.18 (0.38), residues: 183
  loop :  0.03 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B  68 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  215 ASP cc_start: 0.8677 (t0) cc_final: 0.8338 (t0)
REVERT: A  339 TYR cc_start: 0.8663 (m-80) cc_final: 0.7970 (m-80)
REVERT: B   43 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8468 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 109
  average time/residue: 0.1971
  time to fit residues: 28.6205
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  192 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.140446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.122018 restraints weight = 9854.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.02
r_work: 0.3439 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6792  Z= 0.165
  Angle     :  0.448   6.624   9276  Z= 0.237
  Chirality :  0.039   0.135   1104
  Planarity :  0.003   0.027   1164
  Dihedral  :  4.571  72.538    972
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.24 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.29), residues: 885
  helix:  2.70 (0.26), residues: 408
  sheet: -0.12 (0.38), residues: 181
  loop :  0.04 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.005   0.000   ARG R 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3779.02 seconds
wall clock time: 65 minutes 38.40 seconds (3938.40 seconds total)