Starting phenix.real_space_refine
on Wed Mar 12 04:40:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wu1_37849/03_2025/8wu1_37849.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      31      5.16       5
     C    4648      2.51       5
     N    1226      2.21       5
     O    1338      1.98       5
     F       1      1.80       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: 7250
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2577
          Classifications: {'peptide': 358}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 330}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 324
          Unresolved non-hydrogen dihedrals: 212
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 176
    Chain: "H"
      Number of atoms: 1314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1314
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 184}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 210
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 97
    Chain: "L"
      Number of atoms: 1191
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1191
          Classifications: {'peptide': 183}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 228
          Unresolved non-hydrogen angles: 286
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 151
    Chain: "R"
      Number of atoms: 2139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2139
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 8, 'TRANS': 271}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 132
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 48
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Classifications: {'peptide': 1}
  Time building chain proxies: 5.27, per 1000 atoms: 0.73
  Number of scatterers: 7250
  At special positions: 0
  Unit cell: (151.59, 102.3, 88.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      31     16.00
     P       6     15.00
     F       1      9.00
     O    1338      8.00
     N    1226      7.00
     C    4648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 257 " - pdb=" SG  CYS R 264 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1922

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      26.2% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'C' and resid 98 through 108
    Processing helix  chain 'C' and resid 159 through 161
      No H-bonds generated for 'chain 'C' and resid 159 through 161'
    Processing helix  chain 'H' and resid 65 through 68
      removed outlier: 3.894A  pdb=" N   LYS H  68 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 65 through 68'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 4.039A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 164 through 168
    Processing helix  chain 'L' and resid 183 through 187
      removed outlier: 3.944A  pdb=" N   TYR L 187 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 141
      removed outlier: 4.100A  pdb=" N   LEU R 117 " --> pdb=" O   PRO R 113 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ALA R 118 " --> pdb=" O   SER R 114 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 150
      removed outlier: 4.021A  pdb=" N   CYS R 149 " --> pdb=" O   ARG R 145 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ARG R 150 " --> pdb=" O   SER R 146 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 145 through 150'
    Processing helix  chain 'R' and resid 150 through 179
    Processing helix  chain 'R' and resid 187 through 220
    Processing helix  chain 'R' and resid 222 through 228
      removed outlier: 4.034A  pdb=" N   ARG R 226 " --> pdb=" O   LEU R 222 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL R 228 " --> pdb=" O   TYR R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 229 through 250
    Processing helix  chain 'R' and resid 251 through 253
      No H-bonds generated for 'chain 'R' and resid 251 through 253'
    Processing helix  chain 'R' and resid 273 through 309
    Processing helix  chain 'R' and resid 340 through 369
      Proline residue:  R 358  - end of helix
      removed outlier: 3.556A  pdb=" N   ALA R 361 " --> pdb=" O   GLY R 357 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 374 through 399
      Proline residue:  R 394  - end of helix
    Processing helix  chain 'R' and resid 401 through 408
    Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 117
    Processing sheet with id=AA2, first strand: chain 'C' and resid 26 through 28
    Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 87
      removed outlier: 7.217A  pdb=" N   LEU C  79 " --> pdb=" O   PHE C  61 " (cutoff:3.500A)
      removed outlier: 9.178A  pdb=" N   PHE C  61 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL C  81 " --> pdb=" O   CYS C  59 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   CYS C  59 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ASN C  83 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   LEU C  57 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   VAL C  55 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 129
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 188
      removed outlier: 3.769A  pdb=" N   SER C 202 " --> pdb=" O   ASN C 217 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209
      removed outlier: 3.527A  pdb=" N   PHE C 349 " --> pdb=" O   TYR C 321 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   LEU C 351 " --> pdb=" O   VAL C 319 " (cutoff:3.500A)
      removed outlier: 9.405A  pdb=" N   VAL C 319 " --> pdb=" O   LEU C 351 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS C 230 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLN C 237 " --> pdb=" O   PRO C 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 8 through 10
    Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.419A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   ARG H 103 " --> pdb=" O   LEU H 110 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   LEU H 110 " --> pdb=" O   ARG H 103 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.419A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 133
      removed outlier: 5.878A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   SER H 187 " --> pdb=" O   ALA H 178 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ALA H 178 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   SER H 189 " --> pdb=" O   PHE H 176 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 160 through 163
      removed outlier: 3.509A  pdb=" N   LYS H 219 " --> pdb=" O   CYS H 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 12 through 14
      removed outlier: 6.515A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 12 through 14
      removed outlier: 6.515A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 117 through 119
      removed outlier: 3.536A  pdb=" N   THR L 181 " --> pdb=" O   ASN L 159 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ASN L 159 " --> pdb=" O   THR L 181 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1068 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1123
        1.31 -     1.43: 1950
        1.43 -     1.56: 4269
        1.56 -     1.68: 26
        1.68 -     1.81: 39
  Bond restraints: 7407
  Sorted by residual:
  bond pdb=" CAX KCA R 501 "
       pdb=" CBC KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.399  1.577 -0.178 2.00e-02 2.50e+03 7.88e+01
  bond pdb=" CAY KCA R 501 "
       pdb=" CAZ KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.402  1.579 -0.177 2.00e-02 2.50e+03 7.86e+01
  bond pdb=" CAV KCA R 501 "
       pdb=" CAW KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.545 -0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" CAS KCA R 501 "
       pdb=" CAT KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.380  1.534 -0.154 2.00e-02 2.50e+03 5.92e+01
  bond pdb=" CAR KCA R 501 "
       pdb=" CAS KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.389  1.542 -0.153 2.00e-02 2.50e+03 5.85e+01
  ... (remaining 7402 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 10036
        2.38 -     4.76: 108
        4.76 -     7.14: 7
        7.14 -     9.53: 4
        9.53 -    11.91: 2
  Bond angle restraints: 10157
  Sorted by residual:
  angle pdb=" CB  TPO R 432 "
        pdb=" OG1 TPO R 432 "
        pdb=" P   TPO R 432 "
      ideal   model   delta    sigma   weight residual
     119.31  107.40   11.91 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" CB  TPO R 431 "
        pdb=" OG1 TPO R 431 "
        pdb=" P   TPO R 431 "
      ideal   model   delta    sigma   weight residual
     119.31  108.34   10.97 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" C   TYR L 141 "
        pdb=" N   PRO L 142 "
        pdb=" CD  PRO L 142 "
      ideal   model   delta    sigma   weight residual
     120.60  112.66    7.94 2.20e+00 2.07e-01 1.30e+01
  angle pdb=" OG1 TPO R 431 "
        pdb=" P   TPO R 431 "
        pdb=" O1P TPO R 431 "
      ideal   model   delta    sigma   weight residual
     100.43  109.61   -9.18 3.00e+00 1.11e-01 9.37e+00
  angle pdb=" OG1 TPO R 432 "
        pdb=" P   TPO R 432 "
        pdb=" O1P TPO R 432 "
      ideal   model   delta    sigma   weight residual
     100.43  109.58   -9.15 3.00e+00 1.11e-01 9.29e+00
  ... (remaining 10152 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.82: 4014
       15.82 -    31.63: 279
       31.63 -    47.44: 62
       47.44 -    63.26: 13
       63.26 -    79.07: 2
  Dihedral angle restraints: 4370
    sinusoidal: 1406
      harmonic: 2964
  Sorted by residual:
  dihedral pdb=" CB  CYS R 257 "
           pdb=" SG  CYS R 257 "
           pdb=" SG  CYS R 264 "
           pdb=" CB  CYS R 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.12   31.12     1      1.00e+01 1.00e-02 1.38e+01
  dihedral pdb=" CA  PHE R 268 "
           pdb=" C   PHE R 268 "
           pdb=" N   PRO R 269 "
           pdb=" CA  PRO R 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  ASP C 260 "
           pdb=" CB  ASP C 260 "
           pdb=" CG  ASP C 260 "
           pdb=" OD1 ASP C 260 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.28   51.28     1      2.00e+01 2.50e-03 8.99e+00
  ... (remaining 4367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 918
       0.040 -    0.080: 220
       0.080 -    0.121: 87
       0.121 -    0.161: 16
       0.161 -    0.201: 1
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CB  THR R 344 "
            pdb=" CA  THR R 344 "
            pdb=" OG1 THR R 344 "
            pdb=" CG2 THR R 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  KCA R 501 "
            pdb=" N   KCA R 501 "
            pdb=" C   KCA R 501 "
            pdb=" CB  KCA R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  VAL H  40 "
            pdb=" N   VAL H  40 "
            pdb=" C   VAL H  40 "
            pdb=" CB  VAL H  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.41e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 1266
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR L 141 "    0.070 5.00e-02 4.00e+02   1.07e-01 1.85e+01
        pdb=" N   PRO L 142 "   -0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO L 142 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO L 142 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 350 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.84e+00
        pdb=" C   VAL R 350 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL R 350 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL R 351 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN L  80 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO L  81 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO L  81 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO L  81 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1263 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 827
        2.75 -     3.28: 7065
        3.28 -     3.82: 11395
        3.82 -     4.36: 12689
        4.36 -     4.90: 22904
  Nonbonded interactions: 54880
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS L  40 "
            pdb=" O   GLU L  82 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OD1 ASP R 272 "
            pdb=" N   GLU R 273 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" NE2 GLN C 130 "
            pdb=" O   ARG C 282 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OD1 ASP C 240 "
            pdb=" NE2 GLN C 248 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" OG  SER R 265 "
            pdb=" O   PHE R 268 "
     model   vdw
     2.267 3.040
  ... (remaining 54875 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.620
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
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      :  0.008   0.178   7407  Z= 0.494
  Angle     :  0.621  11.908  10157  Z= 0.306
  Chirality :  0.043   0.201   1242
  Planarity :  0.005   0.107   1266
  Dihedral  : 11.916  79.075   2439
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.27), residues: 981
  helix:  0.96 (0.33), residues: 248
  sheet: -0.60 (0.28), residues: 318
  loop : -0.93 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 279 
 HIS   0.010   0.001   HIS C 353 
 PHE   0.016   0.001   PHE H 105 
 TYR   0.015   0.001   TYR H 107 
 ARG   0.008   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.756 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7331 (tppt)
REVERT: R  214 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6929 (mpt180)
REVERT: R  400 ARG cc_start: 0.7038 (mmm160) cc_final: 0.6135 (tmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2146
  time to fit residues: 37.6434
Evaluate side-chains
  119 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
** C 237 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.174090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115367 restraints weight = 9832.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.90
r_work: 0.3258 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7407  Z= 0.214
  Angle     :  0.566   9.109  10157  Z= 0.290
  Chirality :  0.043   0.153   1242
  Planarity :  0.004   0.070   1266
  Dihedral  :  5.595  66.064   1104
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  7.20 %
    Favored  : 91.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.27), residues: 981
  helix:  1.12 (0.33), residues: 233
  sheet: -0.28 (0.29), residues: 315
  loop : -0.75 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.021   0.002   PHE H 105 
 TYR   0.019   0.001   TYR H 107 
 ARG   0.005   0.000   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.827 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7521 (tppt)
  outliers start: 11
  outliers final: 8
  residues processed: 132
  average time/residue: 0.2047
  time to fit residues: 36.5745
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  302 HIS
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 55 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4108 r_free = 0.4108 target = 0.175323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.115089 restraints weight = 9933.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 3.00
r_work: 0.3255 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7407  Z= 0.198
  Angle     :  0.538   8.399  10157  Z= 0.275
  Chirality :  0.042   0.161   1242
  Planarity :  0.004   0.055   1266
  Dihedral  :  5.458  64.376   1104
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  9.80 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.27), residues: 981
  helix:  0.96 (0.33), residues: 239
  sheet: -0.07 (0.29), residues: 304
  loop : -0.71 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.024   0.001   PHE L 140 
 TYR   0.019   0.001   TYR C  47 
 ARG   0.005   0.000   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.802 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7446 (tppt)
REVERT: R  213 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7286 (t70)
REVERT: R  400 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6912 (mmt180)
  outliers start: 19
  outliers final: 10
  residues processed: 129
  average time/residue: 0.2047
  time to fit residues: 34.8418
Evaluate side-chains
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  213 ASP
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  377 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0570
   chunk 91 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0770
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.6456

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 178 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.176489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.116529 restraints weight = 9940.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 3.00
r_work: 0.3267 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7407  Z= 0.169
  Angle     :  0.526  10.756  10157  Z= 0.265
  Chirality :  0.042   0.152   1242
  Planarity :  0.004   0.058   1266
  Dihedral  :  5.289  63.347   1104
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.10 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.27), residues: 981
  helix:  1.09 (0.34), residues: 239
  sheet:  0.11 (0.30), residues: 303
  loop : -0.55 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 279 
 HIS   0.003   0.001   HIS C 353 
 PHE   0.017   0.001   PHE R 177 
 TYR   0.018   0.001   TYR R 296 
 ARG   0.006   0.000   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.774 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8240 (tmmt) cc_final: 0.7425 (tppt)
REVERT: R  189 PHE cc_start: 0.7718 (t80) cc_final: 0.7484 (t80)
REVERT: R  209 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8929 (mm)
REVERT: R  214 ARG cc_start: 0.7544 (mtp180) cc_final: 0.6902 (mmt-90)
REVERT: R  247 ILE cc_start: 0.7936 (mm) cc_final: 0.7510 (mt)
REVERT: R  400 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6885 (mmt180)
  outliers start: 18
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2213
  time to fit residues: 38.6172
Evaluate side-chains
  126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 69 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4093 r_free = 0.4093 target = 0.173785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112668 restraints weight = 9898.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 3.02
r_work: 0.3212 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7407  Z= 0.310
  Angle     :  0.563   9.169  10157  Z= 0.289
  Chirality :  0.043   0.154   1242
  Planarity :  0.004   0.060   1266
  Dihedral  :  5.523  62.574   1104
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.83 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.27), residues: 981
  helix:  1.00 (0.34), residues: 240
  sheet:  0.08 (0.29), residues: 313
  loop : -0.50 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 106 
 HIS   0.006   0.001   HIS C 353 
 PHE   0.027   0.002   PHE H 105 
 TYR   0.020   0.001   TYR H 107 
 ARG   0.009   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 2.119 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8402 (tmmt) cc_final: 0.7607 (tppt)
REVERT: R  209 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: R  247 ILE cc_start: 0.7939 (mm) cc_final: 0.7454 (mt)
REVERT: R  277 MET cc_start: 0.7712 (tmm) cc_final: 0.7502 (tmm)
REVERT: R  400 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6375 (tmt-80)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.3127
  time to fit residues: 53.6003
Evaluate side-chains
  130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  128 THR
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4105 r_free = 0.4105 target = 0.175008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.114190 restraints weight = 9825.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 3.01
r_work: 0.3228 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7407  Z= 0.223
  Angle     :  0.534   9.424  10157  Z= 0.273
  Chirality :  0.042   0.161   1242
  Planarity :  0.004   0.062   1266
  Dihedral  :  5.402  62.852   1104
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.13 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.27), residues: 981
  helix:  1.01 (0.34), residues: 241
  sheet:  0.18 (0.29), residues: 299
  loop : -0.54 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 279 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.020   0.001   PHE H 105 
 TYR   0.017   0.001   TYR H 107 
 ARG   0.008   0.000   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: C  160 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7473 (tppt)
REVERT: R  209 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8962 (mm)
REVERT: R  247 ILE cc_start: 0.7850 (mm) cc_final: 0.7415 (mt)
REVERT: R  275 TYR cc_start: 0.8108 (t80) cc_final: 0.7855 (t80)
REVERT: R  277 MET cc_start: 0.7679 (tmm) cc_final: 0.7450 (tmm)
REVERT: R  400 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6403 (tmt-80)
  outliers start: 18
  outliers final: 16
  residues processed: 132
  average time/residue: 0.2854
  time to fit residues: 49.6293
Evaluate side-chains
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  136 LEU
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  243 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 HIS
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0970
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.171451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.111027 restraints weight = 9878.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.99
r_work: 0.3183 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   7407  Z= 0.380
  Angle     :  0.597   9.535  10157  Z= 0.309
  Chirality :  0.044   0.168   1242
  Planarity :  0.004   0.066   1266
  Dihedral  :  5.751  68.651   1104
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.99 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.27), residues: 981
  helix:  0.82 (0.34), residues: 240
  sheet:  0.04 (0.29), residues: 314
  loop : -0.54 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 279 
 HIS   0.008   0.001   HIS C 353 
 PHE   0.032   0.002   PHE H 105 
 TYR   0.022   0.002   TYR H 107 
 ARG   0.009   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.918 
Fit side-chains
REVERT: C   85 GLN cc_start: 0.8562 (tt0) cc_final: 0.8335 (tt0)
REVERT: C  160 LYS cc_start: 0.8289 (tmmt) cc_final: 0.7575 (tppt)
REVERT: R  129 PHE cc_start: 0.7124 (t80) cc_final: 0.6769 (t80)
REVERT: R  209 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: R  400 ARG cc_start: 0.7324 (mmm160) cc_final: 0.6365 (tmt-80)
  outliers start: 24
  outliers final: 19
  residues processed: 132
  average time/residue: 0.2395
  time to fit residues: 42.0220
Evaluate side-chains
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue  167 GLN
Chi-restraints excluded: chain R residue  128 THR
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 HIS
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4081 r_free = 0.4081 target = 0.172745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112008 restraints weight = 9985.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 3.01
r_work: 0.3192 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7407  Z= 0.326
  Angle     :  0.580   9.624  10157  Z= 0.300
  Chirality :  0.043   0.173   1242
  Planarity :  0.004   0.068   1266
  Dihedral  :  5.740  71.059   1104
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.86 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.27), residues: 981
  helix:  0.83 (0.34), residues: 240
  sheet: -0.02 (0.29), residues: 319
  loop : -0.49 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 279 
 HIS   0.006   0.001   HIS C 353 
 PHE   0.027   0.002   PHE H 105 
 TYR   0.021   0.001   TYR R 296 
 ARG   0.009   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 1.263 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8295 (tmmt) cc_final: 0.7618 (tppt)
REVERT: R  129 PHE cc_start: 0.7178 (t80) cc_final: 0.6830 (t80)
REVERT: R  209 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8983 (mm)
REVERT: R  376 LYS cc_start: 0.6430 (ttpt) cc_final: 0.6190 (ttpt)
REVERT: R  400 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6455 (tmt-80)
  outliers start: 17
  outliers final: 16
  residues processed: 128
  average time/residue: 0.2788
  time to fit residues: 46.7644
Evaluate side-chains
  132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 2.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 HIS
Chi-restraints excluded: chain R residue  353 ILE
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0980
   chunk 49 optimal weight:   20.0000
   chunk 11 optimal weight:    0.4980
   chunk 61 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4111 r_free = 0.4111 target = 0.175768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114894 restraints weight = 9904.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.02
r_work: 0.3236 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7407  Z= 0.161
  Angle     :  0.539   9.796  10157  Z= 0.276
  Chirality :  0.042   0.164   1242
  Planarity :  0.004   0.067   1266
  Dihedral  :  5.453  70.140   1104
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.44 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.27), residues: 981
  helix:  1.03 (0.34), residues: 240
  sheet:  0.30 (0.30), residues: 297
  loop : -0.54 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.015   0.001   PHE H 105 
 TYR   0.022   0.001   TYR R 296 
 ARG   0.010   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.876 
Fit side-chains
REVERT: L  167 GLN cc_start: 0.7758 (tt0) cc_final: 0.7131 (tp40)
REVERT: R  129 PHE cc_start: 0.7174 (t80) cc_final: 0.6844 (t80)
REVERT: R  209 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8984 (mm)
REVERT: R  376 LYS cc_start: 0.6435 (ttpt) cc_final: 0.6190 (ttpt)
REVERT: R  400 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6417 (tmt-80)
  outliers start: 14
  outliers final: 11
  residues processed: 130
  average time/residue: 0.2780
  time to fit residues: 49.4031
Evaluate side-chains
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 HIS
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 52 optimal weight:   40.0000
   chunk 71 optimal weight:    9.9990
   chunk 79 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4099 r_free = 0.4099 target = 0.174680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.113382 restraints weight = 10112.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 3.06
r_work: 0.3212 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7407  Z= 0.239
  Angle     :  0.556   9.815  10157  Z= 0.287
  Chirality :  0.042   0.169   1242
  Planarity :  0.004   0.067   1266
  Dihedral  :  5.471  71.488   1104
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.16 %
    Favored  : 79.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 981
  helix:  0.99 (0.34), residues: 240
  sheet:  0.28 (0.30), residues: 300
  loop : -0.49 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 279 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.022   0.001   PHE H 105 
 TYR   0.027   0.001   TYR R 296 
 ARG   0.009   0.001   ARG R 150 

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

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

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1962 Ramachandran restraints generated.
    981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 1.891 
Fit side-chains
REVERT: R  129 PHE cc_start: 0.7171 (t80) cc_final: 0.6861 (t80)
REVERT: R  209 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: R  296 TYR cc_start: 0.7487 (t80) cc_final: 0.7191 (t80)
REVERT: R  400 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6429 (tmt-80)
  outliers start: 15
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2229
  time to fit residues: 39.4457
Evaluate side-chains
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  224 THR
Chi-restraints excluded: chain C residue  228 VAL
Chi-restraints excluded: chain C residue  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
Chi-restraints excluded: chain R residue  209 LEU
Chi-restraints excluded: chain R residue  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  304 HIS
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 67 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0570
   chunk 31 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 50 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    0.8900

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 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 = 0.4103 r_free = 0.4103 target = 0.174984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114716 restraints weight = 9831.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 3.00
r_work: 0.3235 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7407  Z= 0.204
  Angle     :  0.571  14.871  10157  Z= 0.286
  Chirality :  0.042   0.164   1242
  Planarity :  0.004   0.072   1266
  Dihedral  :  5.391  71.374   1104
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.59 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.27), residues: 981
  helix:  1.03 (0.34), residues: 240
  sheet:  0.38 (0.30), residues: 297
  loop : -0.51 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.018   0.001   PHE R 191 
 TYR   0.024   0.001   TYR R 296 
 ARG   0.008   0.000   ARG R 150 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4714.12 seconds
wall clock time: 86 minutes 10.17 seconds (5170.17 seconds total)