Starting phenix.real_space_refine
on Fri Aug 22 19:31:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wu1_37849/08_2025/8wu1_37849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wu1_37849/08_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_37849/08_2025/8wu1_37849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wu1_37849/08_2025/8wu1_37849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wu1_37849/08_2025/8wu1_37849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wu1_37849/08_2025/8wu1_37849.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLU:plan': 19, 'ARG:plan': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 2}
          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, 'GLU:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 5, 'ARG:plan': 3, 'TYR:plan': 2, 'PHE:plan': 2, 'TRP:plan': 1}
          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: {'ASP:plan': 7, 'GLN:plan1': 10, 'ARG:plan': 2, 'TYR:plan': 3, 'GLU:plan': 6, 'PHE:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          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, 'TYR:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'TPO:plan-1': 2}
          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: 1.98, per 1000 atoms: 0.27
  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: 0.79
  Conformation dependent library (CDL) restraints added in 527.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.26
  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: 1.23

  Time building geometry restraints manager: 0.99 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:             1.480
  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:             0.020
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.780
-------------------------------------------------------------------------------
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   7410  Z= 0.381
  Angle     :  0.621  11.908  10163  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 : 7.29
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (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
 ARG   0.008   0.001   ARG R 150 
 TYR   0.015   0.001   TYR H 107 
 PHE   0.016   0.001   PHE H 105 
 TRP   0.008   0.001   TRP R 279 
 HIS   0.010   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00787 ( 7407)
  covalent geometry    : angle       0.62144 (10157)
  SS BOND              : bond        0.00274 (    3)
  SS BOND              : angle       0.32846 (    6)
  hydrogen bonds       : bond        0.10308 (  368)
  hydrogen bonds       : angle       5.48568 ( 1068)

*********************** 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  : 0.251 
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: 0.0918
  time to fit residues: 16.2568
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  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.173395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.114498 restraints weight = 10079.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.93
r_work: 0.3246 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7410  Z= 0.156
  Angle     :  0.570   9.038  10163  Z= 0.293
  Chirality :  0.043   0.152   1242
  Planarity :  0.004   0.070   1266
  Dihedral  :  5.646  65.756   1104
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  7.49 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.27), residues: 981
  helix:  1.09 (0.33), residues: 233
  sheet: -0.33 (0.29), residues: 317
  loop : -0.74 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 150 
 TYR   0.020   0.001   TYR H 107 
 PHE   0.023   0.002   PHE H 105 
 TRP   0.008   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7407)
  covalent geometry    : angle       0.56976 (10157)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.50941 (    6)
  hydrogen bonds       : bond        0.03638 (  368)
  hydrogen bonds       : angle       4.57260 ( 1068)

*********************** 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
  136 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.297 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8304 (tmmt) cc_final: 0.7534 (tppt)
  outliers start: 11
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0876
  time to fit residues: 15.4118
Evaluate side-chains
  125 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 68 optimal weight:   30.0000
   chunk 89 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 55 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4090 r_free = 0.4090 target = 0.172289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.113359 restraints weight = 10016.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.89
r_work: 0.3221 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7410  Z= 0.203
  Angle     :  0.581   8.195  10163  Z= 0.300
  Chirality :  0.043   0.162   1242
  Planarity :  0.004   0.058   1266
  Dihedral  :  5.754  62.694   1104
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.95 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.27), residues: 981
  helix:  0.82 (0.33), residues: 239
  sheet: -0.27 (0.29), residues: 314
  loop : -0.66 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 150 
 TYR   0.020   0.002   TYR H 107 
 PHE   0.029   0.002   PHE H 105 
 TRP   0.010   0.002   TRP R 279 
 HIS   0.007   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 7407)
  covalent geometry    : angle       0.58120 (10157)
  SS BOND              : bond        0.00344 (    3)
  SS BOND              : angle       0.38135 (    6)
  hydrogen bonds       : bond        0.03621 (  368)
  hydrogen bonds       : angle       4.53194 ( 1068)

*********************** 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
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8391 (tmmt) cc_final: 0.7637 (tppt)
REVERT: R  129 PHE cc_start: 0.7128 (t80) cc_final: 0.6804 (t80)
REVERT: R  400 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6797 (mmt180)
  outliers start: 15
  outliers final: 9
  residues processed: 123
  average time/residue: 0.0938
  time to fit residues: 15.2540
Evaluate side-chains
  122 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  164 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  239 LEU
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  377 THR
Chi-restraints excluded: chain R residue  391 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 98 optimal weight:    0.4980
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.175188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.114274 restraints weight = 10054.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 3.05
r_work: 0.3229 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7410  Z= 0.129
  Angle     :  0.539  10.186  10163  Z= 0.273
  Chirality :  0.042   0.150   1242
  Planarity :  0.004   0.057   1266
  Dihedral  :  5.488  62.727   1104
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 12.54 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.27), residues: 981
  helix:  1.05 (0.34), residues: 239
  sheet:  0.05 (0.30), residues: 298
  loop : -0.65 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 150 
 TYR   0.017   0.001   TYR H 107 
 PHE   0.018   0.001   PHE H 105 
 TRP   0.008   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7407)
  covalent geometry    : angle       0.53875 (10157)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       0.38325 (    6)
  hydrogen bonds       : bond        0.03197 (  368)
  hydrogen bonds       : angle       4.31461 ( 1068)

*********************** 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
  137 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.288 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8301 (tmmt) cc_final: 0.7547 (tppt)
REVERT: C  161 ARG cc_start: 0.7868 (ptp90) cc_final: 0.7595 (ptp90)
REVERT: R  129 PHE cc_start: 0.7115 (t80) cc_final: 0.6747 (t80)
REVERT: R  247 ILE cc_start: 0.7993 (mm) cc_final: 0.7521 (mt)
REVERT: R  400 ARG cc_start: 0.7184 (mmm160) cc_final: 0.6288 (tmt-80)
  outliers start: 14
  outliers final: 10
  residues processed: 131
  average time/residue: 0.0866
  time to fit residues: 15.0361
Evaluate side-chains
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  178 HIS
Chi-restraints excluded: chain R residue  197 THR
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 49 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 24 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0770
   chunk 3 optimal weight:    1.9990
   chunk 94 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.176599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.115750 restraints weight = 9951.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.05
r_work: 0.3248 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7410  Z= 0.113
  Angle     :  0.525   8.913  10163  Z= 0.266
  Chirality :  0.041   0.160   1242
  Planarity :  0.004   0.060   1266
  Dihedral  :  5.323  61.889   1104
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.84 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.27), residues: 981
  helix:  1.15 (0.34), residues: 239
  sheet:  0.20 (0.30), residues: 298
  loop : -0.57 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 150 
 TYR   0.015   0.001   TYR R 296 
 PHE   0.017   0.001   PHE R 177 
 TRP   0.008   0.001   TRP R 279 
 HIS   0.003   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7407)
  covalent geometry    : angle       0.52506 (10157)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.52997 (    6)
  hydrogen bonds       : bond        0.03053 (  368)
  hydrogen bonds       : angle       4.16587 ( 1068)

*********************** 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
  134 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.283 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8259 (tmmt) cc_final: 0.7510 (tppt)
REVERT: C  161 ARG cc_start: 0.7873 (ptp90) cc_final: 0.7589 (ptp90)
REVERT: R  247 ILE cc_start: 0.7913 (mm) cc_final: 0.7428 (mt)
REVERT: R  277 MET cc_start: 0.7689 (tmm) cc_final: 0.7477 (tmm)
REVERT: R  400 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6315 (tmt-80)
  outliers start: 11
  outliers final: 9
  residues processed: 129
  average time/residue: 0.0940
  time to fit residues: 15.9319
Evaluate side-chains
  126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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  178 HIS
Chi-restraints excluded: chain R residue  197 THR
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  391 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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**
L 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.174712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113732 restraints weight = 9937.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 3.03
r_work: 0.3225 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7410  Z= 0.156
  Angle     :  0.538   9.526  10163  Z= 0.275
  Chirality :  0.042   0.159   1242
  Planarity :  0.004   0.062   1266
  Dihedral  :  5.395  64.187   1104
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.99 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.27), residues: 981
  helix:  1.05 (0.34), residues: 240
  sheet:  0.21 (0.30), residues: 298
  loop : -0.54 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 150 
 TYR   0.018   0.001   TYR H 107 
 PHE   0.023   0.001   PHE H 105 
 TRP   0.015   0.001   TRP H 106 
 HIS   0.005   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7407)
  covalent geometry    : angle       0.53768 (10157)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       0.46781 (    6)
  hydrogen bonds       : bond        0.03198 (  368)
  hydrogen bonds       : angle       4.23439 ( 1068)

*********************** 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
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.246 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8300 (tmmt) cc_final: 0.7575 (tppt)
REVERT: C  161 ARG cc_start: 0.7869 (ptp90) cc_final: 0.7577 (ptp90)
REVERT: R  376 LYS cc_start: 0.6291 (ttmt) cc_final: 0.5992 (ttpt)
REVERT: R  400 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6372 (tmt-80)
  outliers start: 15
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0802
  time to fit residues: 13.5544
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue  167 GLN
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.175164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114889 restraints weight = 9934.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 3.00
r_work: 0.3241 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7410  Z= 0.125
  Angle     :  0.535   9.984  10163  Z= 0.270
  Chirality :  0.041   0.165   1242
  Planarity :  0.004   0.063   1266
  Dihedral  :  5.327  64.546   1104
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.71 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 981
  helix:  1.08 (0.34), residues: 240
  sheet:  0.31 (0.30), residues: 297
  loop : -0.53 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  19 
 TYR   0.017   0.001   TYR R 296 
 PHE   0.017   0.001   PHE H 105 
 TRP   0.013   0.001   TRP R 279 
 HIS   0.003   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7407)
  covalent geometry    : angle       0.53518 (10157)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       0.47933 (    6)
  hydrogen bonds       : bond        0.03070 (  368)
  hydrogen bonds       : angle       4.13804 ( 1068)

*********************** 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
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.281 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8241 (tmmt) cc_final: 0.7507 (tppt)
REVERT: C  161 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7562 (ptp90)
REVERT: R  376 LYS cc_start: 0.6307 (ttmt) cc_final: 0.6006 (ttpt)
REVERT: R  400 ARG cc_start: 0.7257 (mmm160) cc_final: 0.6396 (tmt-80)
  outliers start: 13
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0799
  time to fit residues: 13.7523
Evaluate side-chains
  132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:   20.0000
   chunk 34 optimal weight:    0.0470
   chunk 7 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.9680

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.174884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114586 restraints weight = 9938.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 3.00
r_work: 0.3236 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7410  Z= 0.133
  Angle     :  0.544   9.899  10163  Z= 0.274
  Chirality :  0.041   0.166   1242
  Planarity :  0.004   0.066   1266
  Dihedral  :  5.338  65.522   1104
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.29 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.27), residues: 981
  helix:  1.03 (0.34), residues: 240
  sheet:  0.37 (0.30), residues: 297
  loop : -0.47 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 285 
 TYR   0.020   0.001   TYR R 296 
 PHE   0.021   0.001   PHE R 177 
 TRP   0.016   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7407)
  covalent geometry    : angle       0.54443 (10157)
  SS BOND              : bond        0.00199 (    3)
  SS BOND              : angle       0.45175 (    6)
  hydrogen bonds       : bond        0.03132 (  368)
  hydrogen bonds       : angle       4.13806 ( 1068)

*********************** 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
  130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.280 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.8236 (tmmt) cc_final: 0.7508 (tppt)
REVERT: R  275 TYR cc_start: 0.8167 (t80) cc_final: 0.7916 (t80)
REVERT: R  376 LYS cc_start: 0.6333 (ttmt) cc_final: 0.6000 (ttpt)
REVERT: R  400 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6404 (tmt-80)
  outliers start: 11
  outliers final: 11
  residues processed: 126
  average time/residue: 0.0793
  time to fit residues: 13.2900
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  142 VAL
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  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 98 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 4 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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**
L 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.172248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111422 restraints weight = 9915.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 3.01
r_work: 0.3191 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7410  Z= 0.218
  Angle     :  0.597   9.995  10163  Z= 0.306
  Chirality :  0.043   0.170   1242
  Planarity :  0.005   0.078   1266
  Dihedral  :  5.667  69.983   1104
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.86 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.27), residues: 981
  helix:  0.89 (0.34), residues: 240
  sheet:  0.13 (0.29), residues: 323
  loop : -0.44 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 161 
 TYR   0.022   0.002   TYR R 296 
 PHE   0.029   0.002   PHE H 105 
 TRP   0.022   0.002   TRP R 279 
 HIS   0.006   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 7407)
  covalent geometry    : angle       0.59692 (10157)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       0.47674 (    6)
  hydrogen bonds       : bond        0.03464 (  368)
  hydrogen bonds       : angle       4.37700 ( 1068)

*********************** 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
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.268 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.7907 (tmmt) cc_final: 0.7258 (tppt)
REVERT: C  240 ASP cc_start: 0.8258 (m-30) cc_final: 0.7992 (m-30)
REVERT: R  400 ARG cc_start: 0.7437 (mmm160) cc_final: 0.6430 (tmt-80)
  outliers start: 15
  outliers final: 15
  residues processed: 128
  average time/residue: 0.0844
  time to fit residues: 14.4984
Evaluate side-chains
  132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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  234 SER
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue  167 GLN
Chi-restraints excluded: chain R residue  178 HIS
Chi-restraints excluded: chain R residue  197 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.174950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.114221 restraints weight = 9901.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.02
r_work: 0.3233 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7410  Z= 0.127
  Angle     :  0.552  10.243  10163  Z= 0.282
  Chirality :  0.042   0.161   1242
  Planarity :  0.004   0.068   1266
  Dihedral  :  5.455  69.841   1104
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.27), residues: 981
  helix:  0.98 (0.34), residues: 240
  sheet:  0.30 (0.30), residues: 309
  loop : -0.47 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 161 
 TYR   0.028   0.001   TYR R 296 
 PHE   0.021   0.001   PHE R 177 
 TRP   0.025   0.001   TRP R 279 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7407)
  covalent geometry    : angle       0.55200 (10157)
  SS BOND              : bond        0.00184 (    3)
  SS BOND              : angle       0.48861 (    6)
  hydrogen bonds       : bond        0.03171 (  368)
  hydrogen bonds       : angle       4.18571 ( 1068)

********************** 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
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C  160 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7182 (tppt)
REVERT: C  238 TYR cc_start: 0.8656 (m-80) cc_final: 0.8413 (m-10)
REVERT: R  296 TYR cc_start: 0.7482 (t80) cc_final: 0.7190 (t80)
REVERT: R  400 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6415 (tmt-80)
  outliers start: 13
  outliers final: 11
  residues processed: 131
  average time/residue: 0.0918
  time to fit residues: 16.0842
Evaluate side-chains
  132 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  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  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 8 optimal weight:    0.0040
   chunk 89 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 47 optimal weight:   30.0000
   chunk 29 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 85 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.5998

-------------------------------------------------------------------------------
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**
L 167 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.173891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.112368 restraints weight = 9929.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 3.04
r_work: 0.3203 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7410  Z= 0.188
  Angle     :  0.604  14.751  10163  Z= 0.304
  Chirality :  0.043   0.167   1242
  Planarity :  0.004   0.068   1266
  Dihedral  :  5.584  71.708   1104
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.73 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.32 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.27), residues: 981
  helix:  0.90 (0.34), residues: 240
  sheet:  0.21 (0.29), residues: 318
  loop : -0.47 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 161 
 TYR   0.024   0.002   TYR R 296 
 PHE   0.025   0.002   PHE H 105 
 TRP   0.029   0.002   TRP R 279 
 HIS   0.006   0.001   HIS C 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7407)
  covalent geometry    : angle       0.60386 (10157)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       0.42576 (    6)
  hydrogen bonds       : bond        0.03361 (  368)
  hydrogen bonds       : angle       4.28786 ( 1068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1991.76 seconds
wall clock time: 34 minutes 42.60 seconds (2082.60 seconds total)