Starting phenix.real_space_refine
on Thu Jul 31 00:10:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tii_41289/07_2025/8tii_41289_neut.cif"
  }
  resolution = 3.0
  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=   0.103
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      25      5.16       5
     C    4149      2.51       5
     N    1101      2.21       5
     O    1256      1.98       5
     H    6420      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12953
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 4794
          Classifications: {'peptide': 297}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 273}
          Chain breaks: 7
    Chain: "H"
      Number of atoms: 3182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3182
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 3116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 3116
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1752
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "R"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 109
          Classifications: {'peptide': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 7.15, per 1000 atoms: 0.55
  Number of scatterers: 12953
  At special positions: 0
  Unit cell: (65.88, 105.84, 128.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P       2     15.00
     O    1256      8.00
     N    1101      7.00
     C    4149      6.00
     H    6420      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 215 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 19 sheets defined
      4.9% alpha, 48.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.887A  pdb=" N   ARG A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 33
      No H-bonds generated for 'chain 'H' and resid 31 through 33'
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 220 through 223
    Processing helix  chain 'L' and resid 122 through 129
      removed outlier: 3.571A  pdb=" N   SER L 128 " --> pdb=" O   SER L 124 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY L 129 " --> pdb=" O   GLN L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
      removed outlier: 3.640A  pdb=" N   GLU L 188 " --> pdb=" O   LYS L 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 184 through 188'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.920A  pdb=" N   GLN N  65 " --> pdb=" O   ASP N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118
      removed outlier: 3.521A  pdb=" N   VAL A  40 " --> pdb=" O   TYR A  21 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A  42 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   THR A  19 " --> pdb=" O   LEU A  42 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   VAL A   8 " --> pdb=" O   SEP R 355 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SEP R 355 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS A  10 " --> pdb=" O   GLU R 353 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.545A  pdb=" N   ILE A 168 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 8.834A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY A 141 " --> pdb=" O   ARG A  62 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   VAL A  53 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   GLN A  85 " --> pdb=" O   VAL A  53 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   CYS A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 187
    Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 258
      removed outlier: 6.365A  pdb=" N   LYS A 250 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
      removed outlier: 8.259A  pdb=" N   ALA A 239 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLN A 237 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA7, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.514A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR H 121 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.514A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.089A  pdb=" N   ALA H 156 " --> pdb=" O   VAL H 203 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL H 203 " --> pdb=" O   ALA H 156 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   GLY H 158 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   VAL H 201 " --> pdb=" O   GLY H 158 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   LEU H 160 " --> pdb=" O   SER H 199 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   SER H 199 " --> pdb=" O   LEU H 160 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   LYS H 162 " --> pdb=" O   LEU H 197 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LEU H 197 " --> pdb=" O   LYS H 162 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 139 through 143
      removed outlier: 5.089A  pdb=" N   ALA H 156 " --> pdb=" O   VAL H 203 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL H 203 " --> pdb=" O   ALA H 156 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   GLY H 158 " --> pdb=" O   VAL H 201 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   VAL H 201 " --> pdb=" O   GLY H 158 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   LEU H 160 " --> pdb=" O   SER H 199 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   SER H 199 " --> pdb=" O   LEU H 160 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   LYS H 162 " --> pdb=" O   LEU H 197 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   LEU H 197 " --> pdb=" O   LYS H 162 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 170 through 173
      removed outlier: 3.538A  pdb=" N   TYR H 213 " --> pdb=" O   VAL H 230 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.791A  pdb=" N   LEU L  12 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.331A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.519A  pdb=" N   ASN L 139 " --> pdb=" O   TYR L 174 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   THR L 179 " --> pdb=" O   GLN L 161 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.519A  pdb=" N   ASN L 139 " --> pdb=" O   TYR L 174 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER L 175 " --> pdb=" O   THR L 165 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 145 through 150
    Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7
    Processing sheet with id=AC1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 4.011A  pdb=" N   GLU N  44 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ALA N  40 " --> pdb=" O   GLU N  44 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    266 hydrogen bonds defined for protein.
    699 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: 5.06

  Time building geometry restraints manager: 4.19 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: 6410
        1.03 -     1.23: 38
        1.23 -     1.42: 2797
        1.42 -     1.62: 3819
        1.62 -     1.82: 34
  Bond restraints: 13098
  Sorted by residual:
  bond pdb=" CG2 TPO R 352 "
       pdb="HG23 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG21 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" CB  TPO R 352 "
       pdb=" HB  TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" CG2 TPO R 352 "
       pdb="HG22 TPO R 352 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" OG1 TPO R 352 "
       pdb=" P   TPO R 352 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.81e+01
  ... (remaining 13093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 23485
        1.97 -     3.94: 120
        3.94 -     5.91: 8
        5.91 -     7.88: 2
        7.88 -     9.85: 2
  Bond angle restraints: 23617
  Sorted by residual:
  angle pdb=" CB  TPO R 352 "
        pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
      ideal   model   delta    sigma   weight residual
     119.31  109.46    9.85 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
        pdb=" CA  ALA L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  127.55   -6.01 1.91e+00 2.74e-01 9.91e+00
  angle pdb=" OG1 TPO R 352 "
        pdb=" P   TPO R 352 "
        pdb=" O1P TPO R 352 "
      ideal   model   delta    sigma   weight residual
     100.43  108.99   -8.56 3.00e+00 1.11e-01 8.14e+00
  angle pdb=" N   PHE L 140 "
        pdb=" CA  PHE L 140 "
        pdb=" C   PHE L 140 "
      ideal   model   delta    sigma   weight residual
     108.34  112.95   -4.61 1.64e+00 3.72e-01 7.90e+00
  angle pdb=" N   MET A 352 "
        pdb=" CA  MET A 352 "
        pdb=" C   MET A 352 "
      ideal   model   delta    sigma   weight residual
     108.19  111.51   -3.32 1.29e+00 6.01e-01 6.63e+00
  ... (remaining 23612 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 5775
       16.33 -    32.66: 343
       32.66 -    49.00: 111
       49.00 -    65.33: 33
       65.33 -    81.66: 3
  Dihedral angle restraints: 6265
    sinusoidal: 3367
      harmonic: 2898
  Sorted by residual:
  dihedral pdb=" CA  TYR H 116 "
           pdb=" C   TYR H 116 "
           pdb=" N   GLY H 117 "
           pdb=" CA  GLY H 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.21  -19.79     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  TRP H 111 "
           pdb=" CB  TRP H 111 "
           pdb=" CG  TRP H 111 "
           pdb=" CD1 TRP H 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  169.86  -79.86     2      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CA  LYS L 170 "
           pdb=" CB  LYS L 170 "
           pdb=" CG  LYS L 170 "
           pdb=" CD  LYS L 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.72  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 6262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 646
       0.034 -    0.068: 256
       0.068 -    0.102: 57
       0.102 -    0.136: 57
       0.136 -    0.169: 3
  Chirality restraints: 1019
  Sorted by residual:
  chirality pdb=" CA  VAL H  40 "
            pdb=" N   VAL H  40 "
            pdb=" C   VAL H  40 "
            pdb=" CB  VAL H  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.18e-01
  chirality pdb=" CA  ILE L  22 "
            pdb=" N   ILE L  22 "
            pdb=" C   ILE L  22 "
            pdb=" CB  ILE L  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  VAL H 203 "
            pdb=" N   VAL H 203 "
            pdb=" C   VAL H 203 "
            pdb=" CB  VAL H 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 1016 not shown)

  Planarity restraints: 1918
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 167 "   -0.023 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO H 168 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO H 168 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 168 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 203 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO H 204 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO H 204 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 204 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 181 "   -0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO A 182 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 182 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 182 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1915 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 655
        2.19 -     2.80: 26747
        2.80 -     3.40: 32962
        3.40 -     4.00: 46376
        4.00 -     4.60: 70629
  Nonbonded interactions: 177369
  Sorted by model distance:
  nonbonded pdb=" O   LYS L 191 "
            pdb=" H   ARG L 212 "
     model   vdw
     1.594 2.450
  nonbonded pdb="HH12 ARG A  25 "
            pdb=" O2P TPO R 352 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" HE2 HIS A 210 "
            pdb=" O   LEU A 300 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" OD1 ASP L 168 "
            pdb=" H   SER L 169 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" O   ALA A 263 "
            pdb=" HG  SER A 266 "
     model   vdw
     1.616 2.450
  ... (remaining 177364 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.230
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     32.620
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:14.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.106   6683  Z= 0.160
  Angle     :  0.557   9.852   9072  Z= 0.298
  Chirality :  0.044   0.169   1019
  Planarity :  0.003   0.034   1143
  Dihedral  : 11.322  81.659   2421
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  7.86 %
    Favored  : 89.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.31), residues: 801
  helix:  0.30 (1.22), residues: 22
  sheet: -0.31 (0.26), residues: 424
  loop : -1.27 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H  50 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.011   0.001   PHE A 277 
 TYR   0.009   0.001   TYR H  36 
 ARG   0.003   0.000   ARG H 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11850 (  229)
  hydrogen bonds       : angle       6.74739 (  699)
  SS BOND              : bond        0.00250 (    5)
  SS BOND              : angle       0.71292 (   10)
  covalent geometry    : bond        0.00326 ( 6678)
  covalent geometry    : angle       0.55645 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7139 (mmp80)
REVERT: A  103 ARG cc_start: 0.6409 (mtt180) cc_final: 0.6023 (mtm110)
REVERT: A  145 GLU cc_start: 0.6270 (tt0) cc_final: 0.6003 (tt0)
REVERT: A  192 MET cc_start: 0.7897 (mtt) cc_final: 0.7461 (mtp)
REVERT: H   15 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7426 (p)
REVERT: L   28 GLN cc_start: 0.7330 (tt0) cc_final: 0.6929 (mp10)
REVERT: L  150 LYS cc_start: 0.6086 (mttt) cc_final: 0.5858 (mmmt)
REVERT: L  162 GLU cc_start: 0.7136 (mp0) cc_final: 0.6933 (mp0)
REVERT: N  104 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.4601 (m-80)
  outliers start: 21
  outliers final: 11
  residues processed: 131
  average time/residue: 1.9990
  time to fit residues: 278.6002
Evaluate side-chains
  86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain L residue  172 SER
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 61 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.5782

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.191509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.151101 restraints weight = 18476.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.14
r_work: 0.3776 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6598
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6683  Z= 0.118
  Angle     :  0.520   4.980   9072  Z= 0.272
  Chirality :  0.045   0.152   1019
  Planarity :  0.004   0.052   1143
  Dihedral  :  7.498  79.129    934
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.07 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.31), residues: 801
  helix:  0.01 (1.13), residues: 22
  sheet: -0.04 (0.27), residues: 412
  loop : -1.32 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 122 
 HIS   0.005   0.001   HIS A 210 
 PHE   0.013   0.001   PHE A 277 
 TYR   0.009   0.001   TYR A 113 
 ARG   0.006   0.000   ARG N  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (  229)
  hydrogen bonds       : angle       5.59133 (  699)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       0.65133 (   10)
  covalent geometry    : bond        0.00280 ( 6678)
  covalent geometry    : angle       0.52019 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  98 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6983 (mmp80)
REVERT: A  145 GLU cc_start: 0.6365 (tt0) cc_final: 0.6151 (tt0)
REVERT: A  192 MET cc_start: 0.7917 (mtt) cc_final: 0.7461 (mtp)
REVERT: A  290 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.6918 (m-30)
REVERT: H   15 VAL cc_start: 0.7607 (OUTLIER) cc_final: 0.7345 (p)
REVERT: L   28 GLN cc_start: 0.7497 (tt0) cc_final: 0.6949 (mp10)
REVERT: L  150 LYS cc_start: 0.6156 (mttt) cc_final: 0.5875 (mmmt)
REVERT: L  162 GLU cc_start: 0.7377 (mp0) cc_final: 0.7148 (mp0)
REVERT: N   36 TRP cc_start: 0.6627 (m100) cc_final: 0.6386 (m100)
REVERT: N  104 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.4420 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 96
  average time/residue: 1.8524
  time to fit residues: 190.5363
Evaluate side-chains
  86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 74 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0370
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.187218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.142406 restraints weight = 18792.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.35
r_work: 0.3826 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.1812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   6683  Z= 0.099
  Angle     :  0.493   4.972   9072  Z= 0.255
  Chirality :  0.044   0.149   1019
  Planarity :  0.005   0.065   1143
  Dihedral  :  7.258  79.284    930
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.76 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.31), residues: 801
  helix: -0.56 (1.00), residues: 24
  sheet:  0.10 (0.27), residues: 418
  loop : -1.26 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  50 
 HIS   0.003   0.001   HIS L 199 
 PHE   0.009   0.001   PHE A 277 
 TYR   0.012   0.001   TYR H 195 
 ARG   0.009   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02937 (  229)
  hydrogen bonds       : angle       5.30337 (  699)
  SS BOND              : bond        0.00336 (    5)
  SS BOND              : angle       0.57761 (   10)
  covalent geometry    : bond        0.00238 ( 6678)
  covalent geometry    : angle       0.49325 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.6308 (tt0) cc_final: 0.5954 (tt0)
REVERT: A  192 MET cc_start: 0.8013 (mtt) cc_final: 0.7521 (mtp)
REVERT: A  290 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.6872 (m-30)
REVERT: H   15 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7294 (p)
REVERT: L   28 GLN cc_start: 0.7478 (tt0) cc_final: 0.6929 (mp10)
REVERT: L  150 LYS cc_start: 0.6113 (mttt) cc_final: 0.5806 (mmmt)
REVERT: N   36 TRP cc_start: 0.6652 (m100) cc_final: 0.6356 (m100)
REVERT: N  104 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.4406 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 95
  average time/residue: 1.6414
  time to fit residues: 168.3066
Evaluate side-chains
  88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 74 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.185476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140208 restraints weight = 18838.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.38
r_work: 0.3777 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6683  Z= 0.125
  Angle     :  0.509   4.655   9072  Z= 0.264
  Chirality :  0.045   0.154   1019
  Planarity :  0.004   0.045   1143
  Dihedral  :  7.287  79.107    930
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.90 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.31), residues: 801
  helix: -0.18 (1.08), residues: 22
  sheet:  0.10 (0.27), residues: 418
  loop : -1.25 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.003   0.001   HIS L 199 
 PHE   0.015   0.002   PHE A 277 
 TYR   0.016   0.001   TYR H 164 
 ARG   0.007   0.000   ARG N  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  229)
  hydrogen bonds       : angle       5.22935 (  699)
  SS BOND              : bond        0.00296 (    5)
  SS BOND              : angle       0.80050 (   10)
  covalent geometry    : bond        0.00302 ( 6678)
  covalent geometry    : angle       0.50829 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 GLU cc_start: 0.6321 (tt0) cc_final: 0.5987 (tt0)
REVERT: A  192 MET cc_start: 0.8019 (mtt) cc_final: 0.7525 (mtp)
REVERT: H    9 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7343 (tt0)
REVERT: H   15 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7236 (p)
REVERT: L   28 GLN cc_start: 0.7533 (tt0) cc_final: 0.6906 (mp10)
REVERT: L  150 LYS cc_start: 0.6164 (mttt) cc_final: 0.5842 (mmmt)
REVERT: N   36 TRP cc_start: 0.6565 (m100) cc_final: 0.6213 (t-100)
REVERT: N  115 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7255 (m)
  outliers start: 27
  outliers final: 14
  residues processed: 96
  average time/residue: 1.5823
  time to fit residues: 164.5738
Evaluate side-chains
  88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.185015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.140054 restraints weight = 18702.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 2.38
r_work: 0.3768 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   6683  Z= 0.136
  Angle     :  0.516   4.580   9072  Z= 0.268
  Chirality :  0.045   0.155   1019
  Planarity :  0.004   0.036   1143
  Dihedral  :  7.059  79.201    926
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.86 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.31), residues: 801
  helix: -0.16 (1.08), residues: 22
  sheet:  0.09 (0.27), residues: 416
  loop : -1.28 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.003   0.001   HIS L 199 
 PHE   0.012   0.002   PHE A 277 
 TYR   0.020   0.001   TYR H 164 
 ARG   0.004   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  229)
  hydrogen bonds       : angle       5.22003 (  699)
  SS BOND              : bond        0.00314 (    5)
  SS BOND              : angle       0.83879 (   10)
  covalent geometry    : bond        0.00326 ( 6678)
  covalent geometry    : angle       0.51598 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1571 (OUTLIER) cc_final: 0.1312 (p)
REVERT: A  192 MET cc_start: 0.8061 (mtt) cc_final: 0.7586 (mtp)
REVERT: H   15 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7233 (p)
REVERT: H  223 ASN cc_start: 0.7224 (p0) cc_final: 0.6968 (m-40)
REVERT: L   28 GLN cc_start: 0.7502 (tt0) cc_final: 0.6889 (mp10)
REVERT: L  150 LYS cc_start: 0.6185 (mttt) cc_final: 0.5847 (mmmt)
REVERT: N   36 TRP cc_start: 0.6520 (m100) cc_final: 0.6192 (t-100)
REVERT: N  104 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.4363 (m-80)
REVERT: N  115 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7237 (m)
  outliers start: 26
  outliers final: 17
  residues processed: 93
  average time/residue: 1.6935
  time to fit residues: 170.3091
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  164 TYR
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  171 ASP
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 42 optimal weight:    0.3980
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.189025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.148307 restraints weight = 18781.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 2.20
r_work: 0.3788 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   6683  Z= 0.142
  Angle     :  0.525   4.569   9072  Z= 0.273
  Chirality :  0.045   0.158   1019
  Planarity :  0.004   0.036   1143
  Dihedral  :  7.040  79.190    926
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.41 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.31), residues: 801
  helix: -0.04 (1.08), residues: 22
  sheet:  0.04 (0.27), residues: 419
  loop : -1.25 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.012   0.002   PHE A 277 
 TYR   0.019   0.001   TYR H 164 
 ARG   0.003   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  229)
  hydrogen bonds       : angle       5.22994 (  699)
  SS BOND              : bond        0.00322 (    5)
  SS BOND              : angle       0.90248 (   10)
  covalent geometry    : bond        0.00342 ( 6678)
  covalent geometry    : angle       0.52437 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1392 (OUTLIER) cc_final: 0.1163 (p)
REVERT: A  192 MET cc_start: 0.8058 (mtt) cc_final: 0.7590 (mtp)
REVERT: H    9 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7280 (tt0)
REVERT: H   15 VAL cc_start: 0.7529 (OUTLIER) cc_final: 0.7292 (p)
REVERT: H  223 ASN cc_start: 0.7227 (p0) cc_final: 0.6954 (m-40)
REVERT: L   28 GLN cc_start: 0.7504 (tt0) cc_final: 0.6921 (mp10)
REVERT: L  150 LYS cc_start: 0.6116 (mttt) cc_final: 0.5800 (mmmt)
REVERT: N  104 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.4378 (m-80)
REVERT: N  115 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.7093 (m)
  outliers start: 27
  outliers final: 16
  residues processed: 92
  average time/residue: 1.5552
  time to fit residues: 155.2159
Evaluate side-chains
  88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue    9 GLU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  115 SER
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.185148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140130 restraints weight = 18745.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.38
r_work: 0.3770 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6683  Z= 0.122
  Angle     :  0.509   4.581   9072  Z= 0.264
  Chirality :  0.044   0.154   1019
  Planarity :  0.004   0.037   1143
  Dihedral  :  6.867  79.312    925
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 16.14 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.31), residues: 801
  helix:  0.06 (1.09), residues: 22
  sheet:  0.09 (0.27), residues: 419
  loop : -1.22 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.011   0.001   PHE A 277 
 TYR   0.023   0.001   TYR H 164 
 ARG   0.003   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02883 (  229)
  hydrogen bonds       : angle       5.13134 (  699)
  SS BOND              : bond        0.00304 (    5)
  SS BOND              : angle       0.80915 (   10)
  covalent geometry    : bond        0.00293 ( 6678)
  covalent geometry    : angle       0.50878 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  97 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 68
  time to evaluate  : 1.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1480 (OUTLIER) cc_final: 0.1248 (p)
REVERT: A  170 LYS cc_start: 0.6141 (mtpp) cc_final: 0.5767 (mttt)
REVERT: A  192 MET cc_start: 0.8102 (mtt) cc_final: 0.7654 (mtp)
REVERT: H   15 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7295 (p)
REVERT: H  126 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7132 (p)
REVERT: H  223 ASN cc_start: 0.7269 (p0) cc_final: 0.6970 (m-40)
REVERT: L    5 MET cc_start: 0.6866 (mmm) cc_final: 0.6625 (mmm)
REVERT: L   28 GLN cc_start: 0.7497 (tt0) cc_final: 0.6897 (mp10)
REVERT: L  150 LYS cc_start: 0.6174 (mttt) cc_final: 0.5838 (mmmt)
REVERT: N  104 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.4346 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 91
  average time/residue: 1.5230
  time to fit residues: 150.7251
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  164 TYR
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  115 SER
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  171 ASP
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.190181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.149585 restraints weight = 18555.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.18
r_work: 0.3803 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3657 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6582
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6683  Z= 0.118
  Angle     :  0.504   4.394   9072  Z= 0.261
  Chirality :  0.045   0.152   1019
  Planarity :  0.004   0.041   1143
  Dihedral  :  6.779  79.230    925
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.55 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.31), residues: 801
  helix:  0.22 (1.04), residues: 24
  sheet:  0.20 (0.27), residues: 409
  loop : -1.29 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.003   0.001   HIS H  38 
 PHE   0.011   0.001   PHE A 277 
 TYR   0.023   0.001   TYR H 164 
 ARG   0.002   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02833 (  229)
  hydrogen bonds       : angle       5.06649 (  699)
  SS BOND              : bond        0.00307 (    5)
  SS BOND              : angle       0.84501 (   10)
  covalent geometry    : bond        0.00284 ( 6678)
  covalent geometry    : angle       0.50385 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1500 (OUTLIER) cc_final: 0.1269 (p)
REVERT: A  170 LYS cc_start: 0.6093 (mtpp) cc_final: 0.5718 (mttt)
REVERT: A  192 MET cc_start: 0.8106 (mtt) cc_final: 0.7660 (mtp)
REVERT: A  290 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.6649 (m-30)
REVERT: H   15 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (p)
REVERT: H  126 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7071 (p)
REVERT: H  223 ASN cc_start: 0.7316 (p0) cc_final: 0.6994 (m-40)
REVERT: L   28 GLN cc_start: 0.7506 (tt0) cc_final: 0.6937 (mp10)
REVERT: L  150 LYS cc_start: 0.6122 (mttt) cc_final: 0.5818 (mmmt)
REVERT: N  104 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.4398 (m-80)
REVERT: N  115 THR cc_start: 0.7102 (OUTLIER) cc_final: 0.6772 (m)
  outliers start: 25
  outliers final: 20
  residues processed: 87
  average time/residue: 1.4629
  time to fit residues: 138.9851
Evaluate side-chains
  92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  126 THR
Chi-restraints excluded: chain H residue  164 TYR
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  115 SER
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  171 ASP
Chi-restraints excluded: chain L residue  173 THR
Chi-restraints excluded: chain N residue   35 SER
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 67 optimal weight:    2.9990
   chunk 64 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.3638

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.192999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.152906 restraints weight = 18431.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.4008 rms_B_bonded: 2.17
r_work: 0.3895 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6564
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6683  Z= 0.089
  Angle     :  0.478   4.212   9072  Z= 0.245
  Chirality :  0.044   0.146   1019
  Planarity :  0.004   0.041   1143
  Dihedral  :  6.596  78.987    925
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.10 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.31), residues: 801
  helix:  0.68 (1.10), residues: 24
  sheet:  0.27 (0.27), residues: 413
  loop : -1.17 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.023   0.001   TYR H 164 
 ARG   0.003   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02597 (  229)
  hydrogen bonds       : angle       4.88229 (  699)
  SS BOND              : bond        0.00206 (    5)
  SS BOND              : angle       0.65084 (   10)
  covalent geometry    : bond        0.00215 ( 6678)
  covalent geometry    : angle       0.47741 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1631 (OUTLIER) cc_final: 0.1386 (p)
REVERT: A  192 MET cc_start: 0.8094 (mtt) cc_final: 0.7664 (mtp)
REVERT: A  290 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.6866 (m-30)
REVERT: H   15 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7259 (p)
REVERT: H  164 TYR cc_start: 0.6915 (p90) cc_final: 0.6667 (p90)
REVERT: H  223 ASN cc_start: 0.7315 (p0) cc_final: 0.6985 (m-40)
REVERT: L   28 GLN cc_start: 0.7434 (tt0) cc_final: 0.6994 (mp10)
REVERT: N  104 TYR cc_start: 0.6311 (OUTLIER) cc_final: 0.4445 (m-80)
REVERT: N  115 THR cc_start: 0.7106 (OUTLIER) cc_final: 0.6790 (m)
  outliers start: 23
  outliers final: 15
  residues processed: 95
  average time/residue: 1.4462
  time to fit residues: 149.9280
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0070
   chunk 31 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.192793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.152326 restraints weight = 18464.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.17
r_work: 0.3816 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   6683  Z= 0.100
  Angle     :  0.503   8.935   9072  Z= 0.257
  Chirality :  0.044   0.145   1019
  Planarity :  0.004   0.041   1143
  Dihedral  :  6.496  79.090    924
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.34 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.31), residues: 801
  helix:  0.61 (1.07), residues: 24
  sheet:  0.32 (0.27), residues: 413
  loop : -1.14 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.014   0.001   PHE A 277 
 TYR   0.022   0.001   TYR H 164 
 ARG   0.002   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02618 (  229)
  hydrogen bonds       : angle       4.83795 (  699)
  SS BOND              : bond        0.00253 (    5)
  SS BOND              : angle       0.76412 (   10)
  covalent geometry    : bond        0.00247 ( 6678)
  covalent geometry    : angle       0.50235 ( 9062)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   76 is missing expected H atoms. Skipping.
Evaluate side-chains
  94 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 VAL cc_start: 0.1606 (OUTLIER) cc_final: 0.1365 (p)
REVERT: A  192 MET cc_start: 0.8084 (mtt) cc_final: 0.7655 (mtp)
REVERT: A  290 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.6982 (m-30)
REVERT: A  298 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.4911 (m)
REVERT: H   15 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7276 (p)
REVERT: H  223 ASN cc_start: 0.7332 (p0) cc_final: 0.7001 (m-40)
REVERT: L   28 GLN cc_start: 0.7445 (tt0) cc_final: 0.6977 (mp10)
REVERT: N  104 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.4419 (m-80)
REVERT: N  115 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6809 (m)
  outliers start: 22
  outliers final: 15
  residues processed: 90
  average time/residue: 1.4555
  time to fit residues: 142.8823
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   22 ARG
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   39 TRP
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue  111 TRP
Chi-restraints excluded: chain H residue  164 TYR
Chi-restraints excluded: chain H residue  203 VAL
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   57 SER
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain N residue   52 ARG
Chi-restraints excluded: chain N residue   79 VAL
Chi-restraints excluded: chain N residue  104 TYR
Chi-restraints excluded: chain N residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
L 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.187975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.143957 restraints weight = 18614.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.36
r_work: 0.3819 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6495
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6683  Z= 0.102
  Angle     :  0.500   8.369   9072  Z= 0.255
  Chirality :  0.044   0.146   1019
  Planarity :  0.004   0.041   1143
  Dihedral  :  6.469  79.576    924
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.21 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.31), residues: 801
  helix:  0.62 (1.07), residues: 24
  sheet:  0.34 (0.27), residues: 413
  loop : -1.13 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  50 
 HIS   0.002   0.001   HIS H  38 
 PHE   0.009   0.001   PHE A 277 
 TYR   0.022   0.001   TYR H 164 
 ARG   0.002   0.000   ARG L 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02625 (  229)
  hydrogen bonds       : angle       4.77999 (  699)
  SS BOND              : bond        0.00279 (    5)
  SS BOND              : angle       0.86022 (   10)
  covalent geometry    : bond        0.00250 ( 6678)
  covalent geometry    : angle       0.49934 ( 9062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10620.62 seconds
wall clock time: 181 minutes 6.48 seconds (10866.48 seconds total)