Starting phenix.real_space_refine
on Thu Jun 12 00:57:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzj_41760/06_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_41760/06_2025/8tzj_41760.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_2025/8tzj_41760.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzj_41760/06_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-5710/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: 6.76, per 1000 atoms: 0.51
  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: 3.66
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.01
  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: 4.79

  Time building geometry restraints manager: 4.40 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:             0.730
  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:         0.100
  Set scattering table:                    0.130
  Process input model:                     31.480
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.510
-------------------------------------------------------------------------------
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  : 1.082 
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: 0.6976
  time to fit residues: 136.3330
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  : 0.965 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 49 optimal weight:    0.0010
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.8988

-------------------------------------------------------------------------------
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
** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.111958 restraints weight = 27631.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.116512 restraints weight = 13807.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.119419 restraints weight = 8491.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6684  Z= 0.154
  Angle     :  0.608   6.588   9050  Z= 0.304
  Chirality :  0.037   0.150   1074
  Planarity :  0.004   0.037   1130
  Dihedral  :  8.576 114.794    940
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  7.94 %
    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:  2.01 (0.29), residues: 834
  helix:  2.49 (0.22), residues: 526
  sheet: -0.67 (0.76), residues: 56
  loop : -0.73 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 298 
 HIS   0.017   0.001   HIS A  97 
 PHE   0.015   0.001   PHE A 192 
 TYR   0.011   0.002   TYR C 250 
 ARG   0.005   0.001   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06029 (  410)
  hydrogen bonds       : angle       4.32570 ( 1206)
  covalent geometry    : bond        0.00346 ( 6684)
  covalent geometry    : angle       0.60838 ( 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
  97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  302 LEU cc_start: 0.8304 (mt) cc_final: 0.8100 (tt)
REVERT: D  300 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7217 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 96
  average time/residue: 0.5289
  time to fit residues: 63.8789
Evaluate side-chains
  83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 80 optimal weight:    0.0670
   chunk 20 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6922

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.130357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112240 restraints weight = 27727.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116832 restraints weight = 13657.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.119804 restraints weight = 8331.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6684  Z= 0.130
  Angle     :  0.529   6.494   9050  Z= 0.261
  Chirality :  0.036   0.146   1074
  Planarity :  0.003   0.031   1130
  Dihedral  :  8.058 118.170    940
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.38 %
    Favored  : 90.29 %
  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:  2.21 (0.29), residues: 834
  helix:  2.65 (0.22), residues: 526
  sheet: -0.72 (0.74), residues: 56
  loop : -0.65 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 298 
 HIS   0.012   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        0.05172 (  410)
  hydrogen bonds       : angle       4.01606 ( 1206)
  covalent geometry    : bond        0.00266 ( 6684)
  covalent geometry    : angle       0.52881 ( 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
  96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  300 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7190 (mt-10)
  outliers start: 9
  outliers final: 5
  residues processed: 96
  average time/residue: 0.5316
  time to fit residues: 63.4671
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  : 0.926 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.127859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.109776 restraints weight = 28004.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.114262 restraints weight = 14056.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.117145 restraints weight = 8618.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6684  Z= 0.136
  Angle     :  0.535   6.041   9050  Z= 0.264
  Chirality :  0.036   0.148   1074
  Planarity :  0.004   0.062   1130
  Dihedral  :  8.019 120.816    940
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  9.41 %
    Favored  : 89.41 %
  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:  2.73 (0.22), residues: 526
  sheet: -0.95 (0.71), residues: 56
  loop : -0.60 (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   0.013   0.001   PHE D 189 
 TYR   0.011   0.002   TYR C 250 
 ARG   0.004   0.000   ARG D 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  410)
  hydrogen bonds       : angle       3.92368 ( 1206)
  covalent geometry    : bond        0.00302 ( 6684)
  covalent geometry    : angle       0.53488 ( 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
  101 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.5346
  time to fit residues: 68.5774
Evaluate side-chains
  89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 27 optimal weight:    0.0000
   chunk 80 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.6584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.110432 restraints weight = 27858.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.114894 restraints weight = 13818.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117811 restraints weight = 8349.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6684  Z= 0.114
  Angle     :  0.520   6.255   9050  Z= 0.254
  Chirality :  0.036   0.145   1074
  Planarity :  0.003   0.028   1130
  Dihedral  :  7.888 122.697    940
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 10.59 %
    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:  2.41 (0.30), residues: 834
  helix:  2.84 (0.22), residues: 526
  sheet: -0.97 (0.71), residues: 56
  loop : -0.53 (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 C 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04511 (  410)
  hydrogen bonds       : angle       3.80202 ( 1206)
  covalent geometry    : bond        0.00250 ( 6684)
  covalent geometry    : angle       0.51981 ( 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
  94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 93
  average time/residue: 0.4814
  time to fit residues: 57.6154
Evaluate side-chains
  83 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
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   77 ASN
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:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
C  77 ASN
** D 227 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 = 0.3561 r_free = 0.3561 target = 0.124516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.105629 restraints weight = 28499.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110229 restraints weight = 14262.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113250 restraints weight = 8805.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6684  Z= 0.146
  Angle     :  0.538   6.013   9050  Z= 0.265
  Chirality :  0.036   0.146   1074
  Planarity :  0.003   0.027   1130
  Dihedral  :  7.985 126.425    940
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 11.18 %
    Favored  : 87.65 %
  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: -1.01 (0.70), residues: 56
  loop : -0.54 (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   0.003   0.000   ARG B  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  410)
  hydrogen bonds       : angle       3.86819 ( 1206)
  covalent geometry    : bond        0.00337 ( 6684)
  covalent geometry    : angle       0.53810 ( 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
  94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 93
  average time/residue: 0.6399
  time to fit residues: 76.2316
Evaluate side-chains
  84 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 2.120 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN
** D 227 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 = 0.3561 r_free = 0.3561 target = 0.124669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106177 restraints weight = 28133.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110682 restraints weight = 14300.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.113620 restraints weight = 8843.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4003

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= 0.130
  Angle     :  0.535   6.013   9050  Z= 0.262
  Chirality :  0.035   0.147   1074
  Planarity :  0.003   0.025   1130
  Dihedral  :  7.953 127.734    940
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.32 %
    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:  2.40 (0.30), residues: 834
  helix:  2.84 (0.22), residues: 526
  sheet: -0.99 (0.71), residues: 56
  loop : -0.55 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 298 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.009   0.001   PHE D  32 
 TYR   0.011   0.001   TYR C 250 
 ARG   0.006   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  410)
  hydrogen bonds       : angle       3.80505 ( 1206)
  covalent geometry    : bond        0.00297 ( 6684)
  covalent geometry    : angle       0.53489 ( 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
  89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 1.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 89
  average time/residue: 0.7293
  time to fit residues: 86.3565
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  : 1.750 
-------------------------------------------------------------------------------
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  267 LEU
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:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 285 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.105911 restraints weight = 28220.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110424 restraints weight = 14207.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.113414 restraints weight = 8744.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4183

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= 0.131
  Angle     :  0.534   6.655   9050  Z= 0.260
  Chirality :  0.036   0.147   1074
  Planarity :  0.004   0.073   1130
  Dihedral  :  7.968 131.984    940
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.47 %
    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: -0.96 (0.71), residues: 56
  loop : -0.53 (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   0.011   0.001   PHE B  13 
 TYR   0.011   0.001   TYR D 250 
 ARG   0.013   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  410)
  hydrogen bonds       : angle       3.76074 ( 1206)
  covalent geometry    : bond        0.00299 ( 6684)
  covalent geometry    : angle       0.53392 ( 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
  94 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 94
  average time/residue: 0.6220
  time to fit residues: 75.2493
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  : 1.178 
-------------------------------------------------------------------------------
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  267 LEU
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:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
D 225 ASN
** D 285 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 = 0.3546 r_free = 0.3546 target = 0.123711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.104821 restraints weight = 28264.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109418 restraints weight = 14164.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.112471 restraints weight = 8724.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4285

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= 0.135
  Angle     :  0.540   6.050   9050  Z= 0.266
  Chirality :  0.036   0.146   1074
  Planarity :  0.004   0.054   1130
  Dihedral  :  7.983 134.093    940
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.91 %
    Favored  : 87.21 %
  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: -0.99 (0.71), residues: 56
  loop : -0.52 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 298 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.010   0.001   PHE B  13 
 TYR   0.011   0.001   TYR C 250 
 ARG   0.009   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  410)
  hydrogen bonds       : angle       3.76819 ( 1206)
  covalent geometry    : bond        0.00312 ( 6684)
  covalent geometry    : angle       0.53974 ( 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: 6
    poor density    : 84
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 6
  residues processed: 90
  average time/residue: 0.4925
  time to fit residues: 56.9520
Evaluate side-chains
  91 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  267 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 49 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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
** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.102960 restraints weight = 28438.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.107353 restraints weight = 14533.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.110257 restraints weight = 9077.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6684  Z= 0.188
  Angle     :  0.582   5.839   9050  Z= 0.291
  Chirality :  0.037   0.148   1074
  Planarity :  0.004   0.062   1130
  Dihedral  :  8.171 138.962    940
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.06 %
    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:  2.31 (0.30), residues: 834
  helix:  2.75 (0.22), residues: 526
  sheet: -1.26 (0.68), residues: 66
  loop : -0.44 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 298 
 HIS   0.005   0.001   HIS A  97 
 PHE   0.014   0.001   PHE B  13 
 TYR   0.013   0.002   TYR D 250 
 ARG   0.010   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  410)
  hydrogen bonds       : angle       3.93760 ( 1206)
  covalent geometry    : bond        0.00448 ( 6684)
  covalent geometry    : angle       0.58165 ( 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
  96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 95
  average time/residue: 0.5268
  time to fit residues: 65.1843
Evaluate side-chains
  89 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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  267 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:    0.4980
   chunk 46 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  80 ASN
** D 285 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 = 0.3539 r_free = 0.3539 target = 0.123313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104834 restraints weight = 27911.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109247 restraints weight = 14043.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.112254 restraints weight = 8727.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.4557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6684  Z= 0.122
  Angle     :  0.541   6.229   9050  Z= 0.265
  Chirality :  0.036   0.146   1074
  Planarity :  0.004   0.056   1130
  Dihedral  :  7.997 137.618    940
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.35 %
    Favored  : 86.76 %
  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:  2.47 (0.30), residues: 834
  helix:  2.91 (0.22), residues: 526
  sheet: -1.06 (0.70), residues: 56
  loop : -0.55 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 298 
 HIS   0.006   0.001   HIS A  97 
 PHE   0.010   0.001   PHE C  32 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.008   0.000   ARG B  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  410)
  hydrogen bonds       : angle       3.76075 ( 1206)
  covalent geometry    : bond        0.00275 ( 6684)
  covalent geometry    : angle       0.54084 ( 9050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4831.78 seconds
wall clock time: 87 minutes 19.26 seconds (5239.26 seconds total)