Starting phenix.real_space_refine
on Thu May 15 17:04:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzj_41760/05_2025/8tzj_41760.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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: 7
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      26      5.16       5
     C    4210      2.51       5
     N    1184      2.21       5
     O    1148      1.98       5
     H    6772      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 3494
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 3495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 3495
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 9, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 3151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 3151
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 4, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "D"
      Number of atoms: 3150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 3150
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 4, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.24, per 1000 atoms: 0.47
  Number of scatterers: 13346
  At special positions: 0
  Unit cell: (70.2, 83.16, 123.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      26     16.00
     P       4     15.00
     Mg      2     11.99
     O    1148      8.00
     N    1184      7.00
     C    4210      6.00
     H    6772      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.26
  Conformation dependent library (CDL) restraints added in 950.2 milliseconds
  

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      65.7% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 58
      removed outlier: 3.504A  pdb=" N   CYS A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
      removed outlier: 3.851A  pdb=" N   ASN A  89 " --> pdb=" O   PHE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 110
    Processing helix  chain 'A' and resid 110 through 116
      removed outlier: 3.980A  pdb=" N   GLU A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 143 through 147
    Processing helix  chain 'A' and resid 148 through 162
    Processing helix  chain 'A' and resid 178 through 196
      removed outlier: 4.041A  pdb=" N   ARG A 184 " --> pdb=" O   GLU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 212
      removed outlier: 3.541A  pdb=" N   VAL A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 58
      removed outlier: 3.504A  pdb=" N   CYS B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
      removed outlier: 3.851A  pdb=" N   ASN B  89 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 110
    Processing helix  chain 'B' and resid 110 through 116
      removed outlier: 3.980A  pdb=" N   GLU B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 134
    Processing helix  chain 'B' and resid 143 through 147
    Processing helix  chain 'B' and resid 148 through 162
    Processing helix  chain 'B' and resid 178 through 196
      removed outlier: 4.041A  pdb=" N   ARG B 184 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 212
      removed outlier: 3.542A  pdb=" N   VAL B 209 " --> pdb=" O   ASP B 205 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 47
    Processing helix  chain 'C' and resid 50 through 85
      removed outlier: 3.739A  pdb=" N   LEU C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   THR C  57 " --> pdb=" O   GLY C  53 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU C  58 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      Proline residue:  C  68  - end of helix
    Processing helix  chain 'C' and resid 188 through 229
      removed outlier: 3.836A  pdb=" N   ALA C 194 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 240
      removed outlier: 3.507A  pdb=" N   GLY C 240 " --> pdb=" O   MET C 236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 287
      Proline residue:  C 249  - end of helix
      removed outlier: 4.135A  pdb=" N   GLY C 278 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA C 279 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA C 282 " --> pdb=" O   GLY C 278 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU C 283 " --> pdb=" O   ALA C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 325
      removed outlier: 3.676A  pdb=" N   LEU C 302 " --> pdb=" O   TRP C 298 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA C 316 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS C 325 " --> pdb=" O   LYS C 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 48
      removed outlier: 4.254A  pdb=" N   TRP D  48 " --> pdb=" O   PHE D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 85
      removed outlier: 3.870A  pdb=" N   LEU D  56 " --> pdb=" O   LEU D  52 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   THR D  57 " --> pdb=" O   GLY D  53 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU D  58 " --> pdb=" O   ASN D  54 " (cutoff:3.500A)
      Proline residue:  D  68  - end of helix
    Processing helix  chain 'D' and resid 188 through 229
      removed outlier: 3.509A  pdb=" N   ASP D 193 " --> pdb=" O   PHE D 189 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU D 209 " --> pdb=" O   SER D 205 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET D 210 " --> pdb=" O   LEU D 206 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLY D 219 " --> pdb=" O   PHE D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 229 through 240
    Processing helix  chain 'D' and resid 242 through 288
      Proline residue:  D 249  - end of helix
      removed outlier: 4.049A  pdb=" N   GLY D 278 " --> pdb=" O   ILE D 274 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ALA D 279 " --> pdb=" O   LEU D 275 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU D 286 " --> pdb=" O   ALA D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 325
      removed outlier: 3.697A  pdb=" N   ALA D 316 " --> pdb=" O   GLY D 312 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LYS D 325 " --> pdb=" O   LYS D 321 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
      removed outlier: 3.900A  pdb=" N   ILE A  11 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18
      removed outlier: 6.351A  pdb=" N   VAL A  16 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS A  29 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU A  27 " --> pdb=" O   LYS A  18 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40
      removed outlier: 6.045A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA A 170 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY A  91 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   ASP A 171 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL A  93 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44
      removed outlier: 6.739A  pdb=" N   GLY A  43 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34
      removed outlier: 3.901A  pdb=" N   ILE B  11 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18
      removed outlier: 6.351A  pdb=" N   VAL B  16 " --> pdb=" O   LYS B  29 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LYS B  29 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU B  27 " --> pdb=" O   LYS B  18 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40
      removed outlier: 6.045A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA B 170 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY B  91 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   ASP B 171 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   VAL B  93 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44
      removed outlier: 6.738A  pdb=" N   GLY B  43 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1206 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: 4.13

  Time building geometry restraints manager: 3.94 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6766
        1.03 -     1.23: 28
        1.23 -     1.42: 2664
        1.42 -     1.61: 3946
        1.61 -     1.81: 52
  Bond restraints: 13456
  Sorted by residual:
  bond pdb=" C4  ADP B 302 "
       pdb=" C5  ADP B 302 "
    ideal  model  delta    sigma   weight residual
    1.490  1.393  0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" C4  ADP A 302 "
       pdb=" C5  ADP A 302 "
    ideal  model  delta    sigma   weight residual
    1.490  1.393  0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" C6  ADP B 302 "
       pdb=" N6  ADP B 302 "
    ideal  model  delta    sigma   weight residual
    1.355  1.447 -0.092 2.00e-02 2.50e+03 2.13e+01
  bond pdb=" C6  ADP A 302 "
       pdb=" N6  ADP A 302 "
    ideal  model  delta    sigma   weight residual
    1.355  1.447 -0.092 2.00e-02 2.50e+03 2.11e+01
  bond pdb=" C5  ADP B 302 "
       pdb=" C6  ADP B 302 "
    ideal  model  delta    sigma   weight residual
    1.490  1.415  0.075 2.00e-02 2.50e+03 1.39e+01
  ... (remaining 13451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 22783
        2.06 -     4.12: 1498
        4.12 -     6.17: 78
        6.17 -     8.23: 6
        8.23 -    10.29: 12
  Bond angle restraints: 24377
  Sorted by residual:
  angle pdb=" N   LYS B  50 "
        pdb=" CA  LYS B  50 "
        pdb=" C   LYS B  50 "
      ideal   model   delta    sigma   weight residual
     111.07  115.88   -4.81 1.07e+00 8.73e-01 2.02e+01
  angle pdb=" N   LYS A  50 "
        pdb=" CA  LYS A  50 "
        pdb=" C   LYS A  50 "
      ideal   model   delta    sigma   weight residual
     111.07  115.85   -4.78 1.07e+00 8.73e-01 2.00e+01
  angle pdb=" N   GLN B  25 "
        pdb=" CA  GLN B  25 "
        pdb=" C   GLN B  25 "
      ideal   model   delta    sigma   weight residual
     108.52  115.37   -6.85 1.63e+00 3.76e-01 1.76e+01
  angle pdb=" N   GLN A  25 "
        pdb=" CA  GLN A  25 "
        pdb=" C   GLN A  25 "
      ideal   model   delta    sigma   weight residual
     108.52  115.34   -6.82 1.63e+00 3.76e-01 1.75e+01
  angle pdb=" CA  ALA A  48 "
        pdb=" C   ALA A  48 "
        pdb=" N   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     117.19  122.78   -5.59 1.50e+00 4.44e-01 1.39e+01
  ... (remaining 24372 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.57: 5969
       26.57 -    53.14: 206
       53.14 -    79.71: 35
       79.71 -   106.28: 4
      106.28 -   132.85: 2
  Dihedral angle restraints: 6216
    sinusoidal: 3431
      harmonic: 2785
  Sorted by residual:
  dihedral pdb=" O2A ADP A 302 "
           pdb=" O3A ADP A 302 "
           pdb=" PA  ADP A 302 "
           pdb=" PB  ADP A 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   72.85 -132.85     1      2.00e+01 2.50e-03 4.03e+01
  dihedral pdb=" O2A ADP B 302 "
           pdb=" O3A ADP B 302 "
           pdb=" PA  ADP B 302 "
           pdb=" PB  ADP B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   72.82 -132.82     1      2.00e+01 2.50e-03 4.03e+01
  dihedral pdb=" O1B ADP B 302 "
           pdb=" O3A ADP B 302 "
           pdb=" PB  ADP B 302 "
           pdb=" PA  ADP B 302 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   45.65 -105.66     1      2.00e+01 2.50e-03 3.05e+01
  ... (remaining 6213 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 920
       0.051 -    0.103: 122
       0.103 -    0.154: 26
       0.154 -    0.206: 2
       0.206 -    0.257: 4
  Chirality restraints: 1074
  Sorted by residual:
  chirality pdb=" C3' ADP A 302 "
            pdb=" C2' ADP A 302 "
            pdb=" C4' ADP A 302 "
            pdb=" O3' ADP A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.77    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" C3' ADP B 302 "
            pdb=" C2' ADP B 302 "
            pdb=" C4' ADP B 302 "
            pdb=" O3' ADP B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.77    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" C2' ADP B 302 "
            pdb=" C1' ADP B 302 "
            pdb=" C3' ADP B 302 "
            pdb=" O2' ADP B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.73    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1071 not shown)

  Planarity restraints: 1944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  18 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.90e+00
        pdb=" C   LYS A  18 "    0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A  18 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A  19 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  18 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.83e+00
        pdb=" C   LYS B  18 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS B  18 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA B  19 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  44 "   -0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   GLY A  44 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLY A  44 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   HIS A  45 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1941 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 230
        2.11 -     2.73: 24131
        2.73 -     3.36: 36922
        3.36 -     3.98: 44593
        3.98 -     4.60: 72553
  Nonbonded interactions: 178429
  Sorted by model distance:
  nonbonded pdb=" HD1 HIS D  36 "
            pdb=" OH  TYR D 252 "
     model   vdw
     1.490 2.450
  nonbonded pdb=" HD1 HIS C  36 "
            pdb=" OH  TYR C 252 "
     model   vdw
     1.537 2.450
  nonbonded pdb=" HE2 PHE B  13 "
            pdb="HD11 LEU B  53 "
     model   vdw
     1.550 2.270
  nonbonded pdb=" HE2 PHE A  13 "
            pdb="HD11 LEU A  53 "
     model   vdw
     1.551 2.270
  nonbonded pdb=" O   ALA D  59 "
            pdb=" HG  SER D  62 "
     model   vdw
     1.645 2.450
  ... (remaining 178424 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 9 through 50 or (resid 51 and (name N or name CA or name C \ 
 or name O or name CB or name OG or name H or name HA or name HB2 or name HB3))  \ 
or resid 52 through 228 or resid 301 through 302))
}
ncs_group {
  reference = (chain 'C' and (resid 27 through 35 or (resid 36 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 
2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ 
E1)) or resid 37 through 330))
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:             0.220
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     28.000
  Find NCS groups from input model:        0.320
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
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      :  0.004   0.097   6684  Z= 0.232
  Angle     :  0.670  10.288   9050  Z= 0.341
  Chirality :  0.040   0.257   1074
  Planarity :  0.003   0.026   1130
  Dihedral  : 12.126 132.849   2450
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.24 %
    Favored  : 96.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.30), residues: 834
  helix:  2.73 (0.23), residues: 508
  sheet: -0.71 (0.77), residues: 56
  loop : -0.67 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  48 
 HIS   0.002   0.001   HIS C  36 
 PHE   0.010   0.001   PHE C  32 
 TYR   0.008   0.001   TYR C 250 
 ARG   0.005   0.000   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17082 (  410)
  hydrogen bonds       : angle       4.74411 ( 1206)
  covalent geometry    : bond        0.00435 ( 6684)
  covalent geometry    : angle       0.66960 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  165 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8343 (mttt) cc_final: 0.8130 (mttm)
REVERT: C  212 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpt)
REVERT: C  302 LEU cc_start: 0.8034 (mt) cc_final: 0.7659 (tt)
REVERT: D   76 LYS cc_start: 0.8437 (tttt) cc_final: 0.8229 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.7012
  time to fit residues: 136.9115
Evaluate side-chains
  90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0010
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 ASN
B 193 ASN
B 221 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.130022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111833 restraints weight = 27632.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.116389 restraints weight = 13820.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.119314 restraints weight = 8495.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6684  Z= 0.162
  Angle     :  0.614   6.855   9050  Z= 0.308
  Chirality :  0.037   0.149   1074
  Planarity :  0.004   0.037   1130
  Dihedral  :  8.644 115.314    940
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.79 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.29), residues: 834
  helix:  2.48 (0.22), residues: 526
  sheet: -0.66 (0.76), residues: 56
  loop : -0.74 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 298 
 HIS   0.020   0.002   HIS A  97 
 PHE   0.015   0.001   PHE D  37 
 TYR   0.011   0.002   TYR C 250 
 ARG   0.006   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05932 (  410)
  hydrogen bonds       : angle       4.35761 ( 1206)
  covalent geometry    : bond        0.00362 ( 6684)
  covalent geometry    : angle       0.61395 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  300 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7236 (mt-10)
  outliers start: 7
  outliers final: 4
  residues processed: 97
  average time/residue: 0.5210
  time to fit residues: 63.2193
Evaluate side-chains
  82 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  208 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 80 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   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  54 ASN
** C  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 225 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111532 restraints weight = 27733.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.116121 restraints weight = 13668.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.119080 restraints weight = 8334.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6684  Z= 0.130
  Angle     :  0.537   6.338   9050  Z= 0.265
  Chirality :  0.036   0.147   1074
  Planarity :  0.003   0.030   1130
  Dihedral  :  8.134 117.540    940
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.82 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.29), residues: 834
  helix:  2.60 (0.22), residues: 526
  sheet: -0.75 (0.74), residues: 56
  loop : -0.66 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 298 
 HIS   0.012   0.002   HIS D 323 
 PHE   0.010   0.001   PHE C 189 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.003   0.000   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05274 (  410)
  hydrogen bonds       : angle       4.07915 ( 1206)
  covalent geometry    : bond        0.00284 ( 6684)
  covalent geometry    : angle       0.53707 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  300 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7197 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 93
  average time/residue: 0.5583
  time to fit residues: 64.5933
Evaluate side-chains
  86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C  77 ASN ** 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 = 0.3618 r_free = 0.3618 target = 0.128781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110558 restraints weight = 27646.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115070 restraints weight = 13708.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.118036 restraints weight = 8381.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6684  Z= 0.133
  Angle     :  0.536   6.080   9050  Z= 0.264
  Chirality :  0.036   0.148   1074
  Planarity :  0.004   0.074   1130
  Dihedral  :  8.023 119.341    940
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.85 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.29), residues: 834
  helix:  2.69 (0.22), residues: 526
  sheet: -0.93 (0.71), residues: 56
  loop : -0.61 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 298 
 HIS   0.010   0.001   HIS A  97 
 PHE   0.014   0.001   PHE D 189 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.007   0.000   ARG D 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04749 (  410)
  hydrogen bonds       : angle       3.93988 ( 1206)
  covalent geometry    : bond        0.00301 ( 6684)
  covalent geometry    : angle       0.53575 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 0.4922
  time to fit residues: 59.2392
Evaluate side-chains
  88 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0980
   chunk 80 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  80 ASN
C  77 ASN
D 225 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.127578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109755 restraints weight = 27960.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.114165 restraints weight = 13898.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116980 restraints weight = 8480.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6684  Z= 0.116
  Angle     :  0.523   6.269   9050  Z= 0.255
  Chirality :  0.035   0.147   1074
  Planarity :  0.003   0.027   1130
  Dihedral  :  7.910 121.059    940
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 10.15 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.30), residues: 834
  helix:  2.80 (0.22), residues: 526
  sheet: -0.96 (0.71), residues: 56
  loop : -0.57 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 298 
 HIS   0.008   0.001   HIS A  97 
 PHE   0.009   0.001   PHE D  32 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.003   0.000   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  410)
  hydrogen bonds       : angle       3.83976 ( 1206)
  covalent geometry    : bond        0.00256 ( 6684)
  covalent geometry    : angle       0.52339 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 99
  average time/residue: 0.4883
  time to fit residues: 61.7583
Evaluate side-chains
  86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue   77 ASN
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.106936 restraints weight = 28491.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111504 restraints weight = 14367.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.114455 restraints weight = 8802.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6684  Z= 0.138
  Angle     :  0.533   6.071   9050  Z= 0.263
  Chirality :  0.036   0.145   1074
  Planarity :  0.003   0.026   1130
  Dihedral  :  7.963 124.447    940
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.18 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.30), residues: 834
  helix:  2.78 (0.22), residues: 526
  sheet: -0.99 (0.70), residues: 56
  loop : -0.58 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 298 
 HIS   0.007   0.001   HIS A  97 
 PHE   0.012   0.001   PHE D 189 
 TYR   0.011   0.001   TYR C 250 
 ARG   0.004   0.000   ARG C 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04603 (  410)
  hydrogen bonds       : angle       3.86873 ( 1206)
  covalent geometry    : bond        0.00315 ( 6684)
  covalent geometry    : angle       0.53329 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 92
  average time/residue: 0.5041
  time to fit residues: 58.8627
Evaluate side-chains
  86 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   chunk 64 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.125804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107511 restraints weight = 28055.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112011 restraints weight = 14047.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.114930 restraints weight = 8690.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6684  Z= 0.112
  Angle     :  0.520   6.166   9050  Z= 0.253
  Chirality :  0.035   0.146   1074
  Planarity :  0.003   0.026   1130
  Dihedral  :  7.864 125.450    940
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.18 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.30), residues: 834
  helix:  2.88 (0.22), residues: 526
  sheet: -0.95 (0.71), residues: 56
  loop : -0.52 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 298 
 HIS   0.007   0.001   HIS A  97 
 PHE   0.010   0.001   PHE D  32 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.002   0.000   ARG C 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04368 (  410)
  hydrogen bonds       : angle       3.74499 ( 1206)
  covalent geometry    : bond        0.00246 ( 6684)
  covalent geometry    : angle       0.52019 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  325 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8440 (mtmm)
  outliers start: 6
  outliers final: 5
  residues processed: 90
  average time/residue: 0.4910
  time to fit residues: 56.0868
Evaluate side-chains
  87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain C residue  208 SER
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   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 285 GLN
D 285 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.124809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.106367 restraints weight = 28273.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.110908 restraints weight = 14237.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.113875 restraints weight = 8739.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6684  Z= 0.127
  Angle     :  0.530   6.420   9050  Z= 0.259
  Chirality :  0.035   0.147   1074
  Planarity :  0.003   0.026   1130
  Dihedral  :  7.929 131.328    940
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.62 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.30), residues: 834
  helix:  2.88 (0.22), residues: 526
  sheet: -0.95 (0.71), residues: 56
  loop : -0.54 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 298 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.011   0.001   PHE B  13 
 TYR   0.011   0.001   TYR C 250 
 ARG   0.003   0.000   ARG C 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04295 (  410)
  hydrogen bonds       : angle       3.77475 ( 1206)
  covalent geometry    : bond        0.00290 ( 6684)
  covalent geometry    : angle       0.52962 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 95
  average time/residue: 0.4747
  time to fit residues: 58.0681
Evaluate side-chains
  87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.105531 restraints weight = 28149.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110008 restraints weight = 14213.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.112972 restraints weight = 8804.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6684  Z= 0.133
  Angle     :  0.545   6.063   9050  Z= 0.266
  Chirality :  0.036   0.148   1074
  Planarity :  0.003   0.029   1130
  Dihedral  :  7.951 133.696    940
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.35 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.30), residues: 834
  helix:  2.91 (0.22), residues: 526
  sheet: -0.91 (0.72), residues: 56
  loop : -0.54 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 298 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.010   0.001   PHE B  13 
 TYR   0.013   0.001   TYR D 250 
 ARG   0.004   0.000   ARG C 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  410)
  hydrogen bonds       : angle       3.75567 ( 1206)
  covalent geometry    : bond        0.00307 ( 6684)
  covalent geometry    : angle       0.54513 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  90 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.8478 (mmm) cc_final: 0.8101 (mmm)
REVERT: D  324 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8169 (mp)
  outliers start: 5
  outliers final: 4
  residues processed: 90
  average time/residue: 0.5182
  time to fit residues: 60.5110
Evaluate side-chains
  92 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain D residue  291 PHE
Chi-restraints excluded: chain D residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
C 285 GLN
D 225 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.120005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.101486 restraints weight = 28414.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105867 restraints weight = 14481.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.108774 restraints weight = 8987.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6684  Z= 0.185
  Angle     :  0.584   5.959   9050  Z= 0.291
  Chirality :  0.037   0.150   1074
  Planarity :  0.004   0.089   1130
  Dihedral  :  8.204 139.614    940
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.21 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.30), residues: 834
  helix:  2.74 (0.22), residues: 526
  sheet: -1.29 (0.68), residues: 66
  loop : -0.47 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 298 
 HIS   0.006   0.002   HIS D 323 
 PHE   0.015   0.001   PHE B  13 
 TYR   0.013   0.002   TYR C 250 
 ARG   0.016   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04679 (  410)
  hydrogen bonds       : angle       3.94770 ( 1206)
  covalent geometry    : bond        0.00441 ( 6684)
  covalent geometry    : angle       0.58382 ( 9050)

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

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

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1668 Ramachandran restraints generated.
    834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER   46 is missing expected H atoms. Skipping.
Residue SER   51 is missing expected H atoms. Skipping.
Residue SER   46 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Residue LYS   28 is missing expected H atoms. Skipping.
Evaluate side-chains
  94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 94
  average time/residue: 0.4727
  time to fit residues: 57.0630
Evaluate side-chains
  87 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  291 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0370
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.105714 restraints weight = 27913.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.110115 restraints weight = 14041.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.113141 restraints weight = 8713.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6684  Z= 0.109
  Angle     :  0.536   6.400   9050  Z= 0.262
  Chirality :  0.035   0.147   1074
  Planarity :  0.003   0.029   1130
  Dihedral  :  7.917 135.865    940
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 12.50 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.30), residues: 834
  helix:  2.96 (0.22), residues: 526
  sheet: -1.17 (0.69), residues: 66
  loop : -0.33 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 298 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.010   0.001   PHE D  32 
 TYR   0.010   0.001   TYR D 250 
 ARG   0.009   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  410)
  hydrogen bonds       : angle       3.72061 ( 1206)
  covalent geometry    : bond        0.00237 ( 6684)
  covalent geometry    : angle       0.53592 ( 9050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3922.30 seconds
wall clock time: 68 minutes 13.51 seconds (4093.51 seconds total)