Starting phenix.real_space_refine
on Sun Apr  5 08:48:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uam_63985/04_2026/9uam_63985.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.034
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: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5803      2.51       5
     N    1531      2.21       5
     O    1652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9046
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2323
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 288, 2317
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
      Conformer: "B"
        Number of residues, atoms: 288, 2317
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
          bond proxies already assigned to first conformer: 2367
    Chain: "B"
      Number of atoms: 1845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1845
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 2576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2576
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 390
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 1778
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1778
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 134
          Unusual residues: {'CLR': 2, 'LTX': 1, 'Y01': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ACYS A 220 " occ=0.84
      ... (10 atoms not shown)
      pdb=" SG BCYS A 220 " occ=0.16
  Time building chain proxies: 2.45, per 1000 atoms: 0.27
  Number of scatterers: 9046
  At special positions: 0
  Unit cell: (86.355, 123.975, 125.685, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1652      8.00
     N    1531      7.00
     C    5803      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 279 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  95 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 306.1 milliseconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 16 sheets defined
      37.1% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 65
      removed outlier: 4.236A  pdb=" N   PHE A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      removed outlier: 3.627A  pdb=" N   GLN A  65 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 99
      removed outlier: 4.100A  pdb=" N   VAL A  75 " --> pdb=" O   THR A  71 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE A  76 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
      removed outlier: 3.953A  pdb=" N   ALA A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 142
    Processing helix  chain 'A' and resid 151 through 174
    Processing helix  chain 'A' and resid 198 through 231
      removed outlier: 3.529A  pdb=" N   ASN A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      Proline residue:  A 213  - end of helix
      removed outlier: 3.749A  pdb=" N   ILE A 224 " --> pdb=" O  ACYS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 272
      Proline residue:  A 262  - end of helix
    Processing helix  chain 'A' and resid 280 through 307
      Proline residue:  A 302  - end of helix
    Processing helix  chain 'A' and resid 309 through 322
    Processing helix  chain 'B' and resid 6 through 32
      removed outlier: 4.276A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 57
      removed outlier: 3.834A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ARG B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU B  56 " --> pdb=" O   GLN B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 100
      removed outlier: 3.862A  pdb=" N   ILE B  97 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 130
      removed outlier: 3.538A  pdb=" N   ASN B 123 " --> pdb=" O   GLN B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 154
      removed outlier: 3.802A  pdb=" N   ALA B 150 " --> pdb=" O   GLN B 146 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLU B 151 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 170
      removed outlier: 3.547A  pdb=" N   ALA B 168 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR B 170 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 204
      removed outlier: 3.690A  pdb=" N   LYS B 195 " --> pdb=" O   TYR B 191 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLU B 196 " --> pdb=" O   PHE B 192 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   PHE B 197 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 3.785A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE B 228 " --> pdb=" O   ALA B 224 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG B 241 " --> pdb=" O   GLN B 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 29 through 35
      removed outlier: 3.745A  pdb=" N   ILE C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 24
      removed outlier: 3.501A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.610A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 51 through 55
      removed outlier: 4.300A  pdb=" N   GLY E  55 " --> pdb=" O   SER E  52 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35
      removed outlier: 6.581A  pdb=" N   LEU B  34 " --> pdb=" O   HIS B  82 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   PHE B  84 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 35
      removed outlier: 6.581A  pdb=" N   LEU B  34 " --> pdb=" O   HIS B  82 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   PHE B  84 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 39
      removed outlier: 7.152A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 52
      removed outlier: 6.813A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   PHE C 335 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER C 331 " --> pdb=" O   PHE C 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.662A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 114
      removed outlier: 3.655A  pdb=" N   VAL C 112 " --> pdb=" O   TYR C 124 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.836A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 189 through 192
      removed outlier: 3.584A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.652A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 250 through 253
      removed outlier: 3.791A  pdb=" N   CYS C 250 " --> pdb=" O   TYR C 264 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU C 252 " --> pdb=" O   MET C 262 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 276 through 277
      removed outlier: 3.523A  pdb=" N   SER C 277 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   CYS C 294 " --> pdb=" O   LEU C 308 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU C 308 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 11
    Processing sheet with id=AB5, first strand: chain 'E' and resid 58 through 59
      removed outlier: 3.656A  pdb=" N   VAL E  96 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 155 through 159
    Processing sheet with id=AB7, first strand: chain 'E' and resid 186 through 189
      removed outlier: 5.814A  pdb=" N   LEU E 187 " --> pdb=" O   LEU E 178 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU E 178 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE E 189 " --> pdb=" O   TRP E 176 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE E 177 " --> pdb=" O   TYR E 228 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1147 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1435
        1.32 -     1.45: 2570
        1.45 -     1.58: 5150
        1.58 -     1.71: 0
        1.71 -     1.83: 87
  Bond restraints: 9242
  Sorted by residual:
  bond pdb=" C22 LTX A 602 "
       pdb=" N3  LTX A 602 "
    ideal  model  delta    sigma   weight residual
    1.331  1.470 -0.139 2.00e-02 2.50e+03 4.86e+01
  bond pdb=" CD1 LTX A 602 "
       pdb=" N2  LTX A 602 "
    ideal  model  delta    sigma   weight residual
    1.349  1.473 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" C8  LTX A 602 "
       pdb=" C9  LTX A 602 "
    ideal  model  delta    sigma   weight residual
    1.446  1.562 -0.116 2.00e-02 2.50e+03 3.35e+01
  bond pdb=" C10 LTX A 602 "
       pdb=" C11 LTX A 602 "
    ideal  model  delta    sigma   weight residual
    1.447  1.551 -0.104 2.00e-02 2.50e+03 2.72e+01
  bond pdb=" C6  LTX A 602 "
       pdb=" C7  LTX A 602 "
    ideal  model  delta    sigma   weight residual
    1.487  1.546 -0.059 2.00e-02 2.50e+03 8.57e+00
  ... (remaining 9237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.43: 12500
        5.43 -    10.87: 26
       10.87 -    16.30: 2
       16.30 -    21.74: 0
       21.74 -    27.17: 3
  Bond angle restraints: 12531
  Sorted by residual:
  angle pdb=" C7  LTX A 602 "
        pdb=" C8  LTX A 602 "
        pdb=" C9  LTX A 602 "
      ideal   model   delta    sigma   weight residual
     123.39  150.56  -27.17 3.00e+00 1.11e-01 8.20e+01
  angle pdb=" C11 LTX A 602 "
        pdb=" C10 LTX A 602 "
        pdb=" C9  LTX A 602 "
      ideal   model   delta    sigma   weight residual
     122.90   95.99   26.91 3.00e+00 1.11e-01 8.04e+01
  angle pdb=" C13 LTX A 602 "
        pdb=" C14 LTX A 602 "
        pdb=" C15 LTX A 602 "
      ideal   model   delta    sigma   weight residual
     127.34  152.59  -25.25 3.00e+00 1.11e-01 7.09e+01
  angle pdb=" C14 LTX A 602 "
        pdb=" C15 LTX A 602 "
        pdb=" C16 LTX A 602 "
      ideal   model   delta    sigma   weight residual
     128.05  112.61   15.44 3.00e+00 1.11e-01 2.65e+01
  angle pdb=" C   ALA A 196 "
        pdb=" N   LYS A 197 "
        pdb=" CA  LYS A 197 "
      ideal   model   delta    sigma   weight residual
     121.54  130.08   -8.54 1.91e+00 2.74e-01 2.00e+01
  ... (remaining 12526 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.98: 5322
       25.98 -    51.96: 277
       51.96 -    77.94: 22
       77.94 -   103.92: 10
      103.92 -   129.90: 7
  Dihedral angle restraints: 5638
    sinusoidal: 2337
      harmonic: 3301
  Sorted by residual:
  dihedral pdb=" CB  CYS E  21 "
           pdb=" SG  CYS E  21 "
           pdb=" SG  CYS E  95 "
           pdb=" CB  CYS E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.89  -60.89     1      1.00e+01 1.00e-02 4.93e+01
  dihedral pdb=" CA  SER A 151 "
           pdb=" C   SER A 151 "
           pdb=" N   ILE A 152 "
           pdb=" CA  ILE A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.35  -21.65     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" C10 CLR A 604 "
           pdb=" C1  CLR A 604 "
           pdb=" C2  CLR A 604 "
           pdb=" C3  CLR A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   73.07 -129.90     1      3.00e+01 1.11e-03 1.75e+01
  ... (remaining 5635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1219
       0.064 -    0.128: 190
       0.128 -    0.192: 17
       0.192 -    0.255: 2
       0.255 -    0.319: 2
  Chirality restraints: 1430
  Sorted by residual:
  chirality pdb=" C13 CLR A 603 "
            pdb=" C12 CLR A 603 "
            pdb=" C14 CLR A 603 "
            pdb=" C17 CLR A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.61   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" C13 CLR A 604 "
            pdb=" C12 CLR A 604 "
            pdb=" C14 CLR A 604 "
            pdb=" C17 CLR A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.62   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" C14 CLR A 604 "
            pdb=" C13 CLR A 604 "
            pdb=" C15 CLR A 604 "
            pdb=" C8  CLR A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.53    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1427 not shown)

  Planarity restraints: 1565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.035 5.00e-02 4.00e+02   5.27e-02 4.44e+00
        pdb=" N   PRO C 236 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO E 236 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 208 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   VAL A 208 "    0.033 2.00e-02 2.50e+03
        pdb=" O   VAL A 208 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY A 209 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1562 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 3165
        2.86 -     3.37: 8305
        3.37 -     3.88: 13974
        3.88 -     4.39: 15311
        4.39 -     4.90: 27771
  Nonbonded interactions: 68526
  Sorted by model distance:
  nonbonded pdb=" C11 LTX A 602 "
            pdb=" C8  LTX A 602 "
     model   vdw
     2.356 2.912
  nonbonded pdb=" O   ALA C 257 "
            pdb=" OD1 ASP C 258 "
     model   vdw
     2.499 3.040
  nonbonded pdb=" C2  CLR A 603 "
            pdb=" C5  CLR A 603 "
     model   vdw
     2.559 2.936
  nonbonded pdb=" O   LEU A 118 "
            pdb=" OD1 ASN A 121 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" OD1 ASP C 153 "
            pdb=" N   ASP C 154 "
     model   vdw
     2.569 3.120
  ... (remaining 68521 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=0.16 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:             2.230
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.520
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
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      :  0.005   0.139   9246  Z= 0.238
  Angle     :  0.869  27.174  12537  Z= 0.400
  Chirality :  0.048   0.319   1430
  Planarity :  0.004   0.053   1565
  Dihedral  : 15.649 129.904   3501
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.25), residues: 1121
  helix:  1.66 (0.27), residues: 387
  sheet: -1.54 (0.31), residues: 267
  loop : -2.37 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 100 
 TYR   0.022   0.002   TYR E 190 
 PHE   0.020   0.001   PHE A 300 
 TRP   0.019   0.002   TRP A 104 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 9242)
  covalent geometry    : angle       0.86885 (12531)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       0.63478 (    6)
  hydrogen bonds       : bond        0.13106 (  413)
  hydrogen bonds       : angle       5.06670 ( 1147)
  Misc. bond           : bond        0.07515 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.7939 (mm) cc_final: 0.7658 (mt)
REVERT: C   46 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6731 (ttp80)
REVERT: C  219 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7488 (mtt-85)
REVERT: C  325 MET cc_start: 0.8265 (mmt) cc_final: 0.8053 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0882
  time to fit residues: 16.3075
Evaluate side-chains
  108 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.171369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.132063 restraints weight = 21655.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 6.55
r_work: 0.3134 rms_B_bonded: 6.35 restraints_weight: 2.0000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9246  Z= 0.132
  Angle     :  0.632  10.988  12537  Z= 0.318
  Chirality :  0.044   0.246   1430
  Planarity :  0.004   0.056   1565
  Dihedral  : 10.029 117.372   1480
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  7.56 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.25), residues: 1121
  helix:  1.92 (0.27), residues: 389
  sheet: -1.41 (0.31), residues: 262
  loop : -2.46 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 100 
 TYR   0.021   0.002   TYR E 190 
 PHE   0.027   0.002   PHE A  93 
 TRP   0.014   0.001   TRP E  46 
 HIS   0.003   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9242)
  covalent geometry    : angle       0.63162 (12531)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       0.60163 (    6)
  hydrogen bonds       : bond        0.04565 (  413)
  hydrogen bonds       : angle       4.49803 ( 1147)
  Misc. bond           : bond        0.00225 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.7854 (mm) cc_final: 0.7562 (mt)
REVERT: C   46 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7943 (ttp80)
REVERT: C  219 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7989 (mtt-85)
REVERT: C  325 MET cc_start: 0.8793 (mmt) cc_final: 0.8591 (tpp)
REVERT: E  230 MET cc_start: 0.8706 (tpp) cc_final: 0.8485 (ttm)
  outliers start: 6
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0936
  time to fit residues: 15.3994
Evaluate side-chains
  111 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  220 ASP
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.174124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.138223 restraints weight = 24828.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 6.33
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3716 r_free = 0.3716    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3716 r_free = 0.3716    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9246  Z= 0.134
  Angle     :  0.605  11.663  12537  Z= 0.309
  Chirality :  0.044   0.224   1430
  Planarity :  0.004   0.057   1565
  Dihedral  :  9.433 118.281   1480
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.01 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.25), residues: 1121
  helix:  2.01 (0.27), residues: 388
  sheet: -1.35 (0.32), residues: 256
  loop : -2.48 (0.25), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 100 
 TYR   0.020   0.001   TYR E 190 
 PHE   0.019   0.001   PHE A  36 
 TRP   0.013   0.001   TRP E  46 
 HIS   0.004   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9242)
  covalent geometry    : angle       0.60529 (12531)
  SS BOND              : bond        0.00199 (    3)
  SS BOND              : angle       0.52358 (    6)
  hydrogen bonds       : bond        0.04445 (  413)
  hydrogen bonds       : angle       4.37843 ( 1147)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.8001 (mm) cc_final: 0.7740 (mt)
REVERT: C   46 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6826 (ttp80)
REVERT: C  219 ARG cc_start: 0.7696 (mtp85) cc_final: 0.7365 (mtt-85)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0928
  time to fit residues: 16.8439
Evaluate side-chains
  115 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  315 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.176600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128560 restraints weight = 24557.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 4.27
r_work: 0.3272 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9246  Z= 0.182
  Angle     :  0.645  12.406  12537  Z= 0.333
  Chirality :  0.046   0.241   1430
  Planarity :  0.004   0.057   1565
  Dihedral  :  9.193 117.735   1480
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.18 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.26), residues: 1121
  helix:  2.01 (0.27), residues: 383
  sheet: -1.45 (0.32), residues: 258
  loop : -2.41 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 100 
 TYR   0.025   0.002   TYR E 190 
 PHE   0.014   0.002   PHE C 241 
 TRP   0.016   0.001   TRP E  46 
 HIS   0.005   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 9242)
  covalent geometry    : angle       0.64498 (12531)
  SS BOND              : bond        0.00200 (    3)
  SS BOND              : angle       0.54524 (    6)
  hydrogen bonds       : bond        0.04918 (  413)
  hydrogen bonds       : angle       4.44951 ( 1147)
  Misc. bond           : bond        0.00044 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   84 ASP cc_start: 0.7561 (t70) cc_final: 0.7359 (t70)
REVERT: A  166 ILE cc_start: 0.7860 (mm) cc_final: 0.7584 (mt)
REVERT: A  300 PHE cc_start: 0.6461 (m-10) cc_final: 0.6218 (m-10)
REVERT: C   45 MET cc_start: 0.8641 (mtt) cc_final: 0.8199 (mtt)
REVERT: C   46 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7568 (ttp80)
REVERT: C  219 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7778 (mtt-85)
  outliers start: 16
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0854
  time to fit residues: 15.4592
Evaluate side-chains
  116 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  220 ASP
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 41 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.180060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128263 restraints weight = 28035.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 4.69
r_work: 0.3289 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9246  Z= 0.117
  Angle     :  0.580  12.404  12537  Z= 0.296
  Chirality :  0.043   0.254   1430
  Planarity :  0.004   0.054   1565
  Dihedral  :  8.870 116.974   1480
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.70 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1121
  helix:  2.25 (0.27), residues: 377
  sheet: -1.44 (0.32), residues: 265
  loop : -2.28 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.016   0.001   TYR A  45 
 PHE   0.010   0.001   PHE A 300 
 TRP   0.014   0.001   TRP C  82 
 HIS   0.002   0.001   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9242)
  covalent geometry    : angle       0.57979 (12531)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       0.41634 (    6)
  hydrogen bonds       : bond        0.04120 (  413)
  hydrogen bonds       : angle       4.29636 ( 1147)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ILE cc_start: 0.7770 (mm) cc_final: 0.7489 (mt)
REVERT: A  300 PHE cc_start: 0.6437 (m-10) cc_final: 0.6228 (m-10)
REVERT: C   45 MET cc_start: 0.8615 (mtt) cc_final: 0.8185 (mtt)
REVERT: C   46 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7716 (ttp80)
REVERT: C  217 MET cc_start: 0.8214 (mpp) cc_final: 0.7971 (pmm)
REVERT: C  219 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7773 (mtt-85)
  outliers start: 18
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0836
  time to fit residues: 15.4712
Evaluate side-chains
  113 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0870
   chunk 71 optimal weight:    8.9990
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.180335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131879 restraints weight = 22946.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 4.03
r_work: 0.3388 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9246  Z= 0.116
  Angle     :  0.571  12.494  12537  Z= 0.291
  Chirality :  0.043   0.262   1430
  Planarity :  0.004   0.055   1565
  Dihedral  :  8.673 116.711   1480
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.04 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.26), residues: 1121
  helix:  2.36 (0.27), residues: 375
  sheet: -1.33 (0.31), residues: 270
  loop : -2.25 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.016   0.001   TYR E 190 
 PHE   0.009   0.001   PHE A 300 
 TRP   0.012   0.001   TRP E  46 
 HIS   0.002   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9242)
  covalent geometry    : angle       0.57083 (12531)
  SS BOND              : bond        0.00132 (    3)
  SS BOND              : angle       0.40511 (    6)
  hydrogen bonds       : bond        0.03970 (  413)
  hydrogen bonds       : angle       4.21645 ( 1147)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  166 ILE cc_start: 0.7755 (mm) cc_final: 0.7481 (mt)
REVERT: C   46 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7611 (ttp80)
REVERT: C  214 ARG cc_start: 0.8893 (ptp-170) cc_final: 0.8502 (mtm110)
REVERT: C  217 MET cc_start: 0.8185 (mpp) cc_final: 0.7895 (pmm)
REVERT: C  219 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7683 (mtt-85)
  outliers start: 18
  outliers final: 14
  residues processed: 124
  average time/residue: 0.0983
  time to fit residues: 16.9446
Evaluate side-chains
  119 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0010
   chunk 24 optimal weight:    0.0670
   chunk 68 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5726

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.181287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133940 restraints weight = 26188.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 4.61
r_work: 0.3331 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9246  Z= 0.109
  Angle     :  0.562  12.869  12537  Z= 0.284
  Chirality :  0.043   0.272   1430
  Planarity :  0.004   0.055   1565
  Dihedral  :  8.423 116.262   1480
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.15 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.26), residues: 1121
  helix:  2.39 (0.27), residues: 375
  sheet: -1.24 (0.32), residues: 268
  loop : -2.19 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.015   0.001   TYR E 190 
 PHE   0.009   0.001   PHE B 215 
 TRP   0.011   0.001   TRP E  46 
 HIS   0.002   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9242)
  covalent geometry    : angle       0.56219 (12531)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.36945 (    6)
  hydrogen bonds       : bond        0.03779 (  413)
  hydrogen bonds       : angle       4.16465 ( 1147)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  166 ILE cc_start: 0.7790 (mm) cc_final: 0.7507 (mt)
REVERT: C   45 MET cc_start: 0.8785 (mtt) cc_final: 0.8192 (mtt)
REVERT: C   46 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7591 (ttp80)
REVERT: C  214 ARG cc_start: 0.8856 (ptp-170) cc_final: 0.8466 (mtm110)
REVERT: C  217 MET cc_start: 0.8215 (mpp) cc_final: 0.7946 (pmm)
REVERT: C  219 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7491 (mtt-85)
REVERT: E   86 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7657 (mtt90)
REVERT: E  139 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8589 (m)
  outliers start: 16
  outliers final: 14
  residues processed: 123
  average time/residue: 0.0905
  time to fit residues: 15.6622
Evaluate side-chains
  121 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue  123 ILE
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  139 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    0.0370
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.7864

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.174885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127009 restraints weight = 27502.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 5.16
r_work: 0.3196 rms_B_bonded: 5.12 restraints_weight: 2.0000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9246  Z= 0.202
  Angle     :  0.654  13.066  12537  Z= 0.337
  Chirality :  0.046   0.280   1430
  Planarity :  0.004   0.059   1565
  Dihedral  :  8.562 116.591   1480
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.94 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.26), residues: 1121
  helix:  2.12 (0.27), residues: 377
  sheet: -1.46 (0.32), residues: 264
  loop : -2.25 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.026   0.002   TYR E 190 
 PHE   0.014   0.002   PHE C 241 
 TRP   0.015   0.001   TRP E  46 
 HIS   0.006   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 9242)
  covalent geometry    : angle       0.65453 (12531)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.48695 (    6)
  hydrogen bonds       : bond        0.04979 (  413)
  hydrogen bonds       : angle       4.41073 ( 1147)
  Misc. bond           : bond        0.00037 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8036 (mtt) cc_final: 0.7593 (mtt)
REVERT: A  166 ILE cc_start: 0.7765 (mm) cc_final: 0.7487 (mt)
REVERT: A  188 LEU cc_start: 0.4895 (mt) cc_final: 0.4342 (pt)
REVERT: A  300 PHE cc_start: 0.6641 (m-10) cc_final: 0.6400 (m-10)
REVERT: C   45 MET cc_start: 0.8876 (mtt) cc_final: 0.8343 (mtt)
REVERT: C   46 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7651 (ttp80)
REVERT: C  217 MET cc_start: 0.8350 (mpp) cc_final: 0.8078 (pmm)
REVERT: C  219 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7787 (mtt-85)
REVERT: E   86 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7737 (mtt90)
  outliers start: 22
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0942
  time to fit residues: 17.0695
Evaluate side-chains
  124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  139 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 47 optimal weight:    0.3980
   chunk 80 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
C  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.177489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.126117 restraints weight = 28288.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 4.65
r_work: 0.3254 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3272
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3272 r_free = 0.3272    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3272
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9246  Z= 0.136
  Angle     :  0.603  13.101  12537  Z= 0.308
  Chirality :  0.044   0.291   1430
  Planarity :  0.004   0.054   1565
  Dihedral  :  8.395 115.277   1480
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.25 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.26), residues: 1121
  helix:  2.24 (0.27), residues: 377
  sheet: -1.39 (0.32), residues: 259
  loop : -2.22 (0.26), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.017   0.001   TYR E 190 
 PHE   0.011   0.001   PHE C 241 
 TRP   0.014   0.001   TRP E  46 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9242)
  covalent geometry    : angle       0.60332 (12531)
  SS BOND              : bond        0.00162 (    3)
  SS BOND              : angle       0.46132 (    6)
  hydrogen bonds       : bond        0.04278 (  413)
  hydrogen bonds       : angle       4.29603 ( 1147)
  Misc. bond           : bond        0.00027 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7921 (mtt) cc_final: 0.7473 (mtt)
REVERT: A  166 ILE cc_start: 0.7776 (mm) cc_final: 0.7499 (mt)
REVERT: A  188 LEU cc_start: 0.4721 (mt) cc_final: 0.4092 (pt)
REVERT: A  300 PHE cc_start: 0.6534 (m-10) cc_final: 0.6292 (m-10)
REVERT: C   45 MET cc_start: 0.8843 (mtt) cc_final: 0.8299 (mtt)
REVERT: C   46 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7604 (ttp80)
REVERT: C  217 MET cc_start: 0.8319 (mpp) cc_final: 0.8073 (pmm)
REVERT: C  219 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7459 (mtt-85)
REVERT: E   72 ASP cc_start: 0.7629 (t0) cc_final: 0.7118 (t0)
REVERT: E   86 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7732 (mtt90)
  outliers start: 19
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0991
  time to fit residues: 17.1172
Evaluate side-chains
  125 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  139 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.178801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.129762 restraints weight = 18700.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 3.73
r_work: 0.3364 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3363
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3363 r_free = 0.3363    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3363
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9246  Z= 0.121
  Angle     :  0.595  13.180  12537  Z= 0.302
  Chirality :  0.044   0.293   1430
  Planarity :  0.004   0.054   1565
  Dihedral  :  8.270 115.027   1480
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.29 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 1121
  helix:  2.32 (0.27), residues: 376
  sheet: -1.33 (0.32), residues: 259
  loop : -2.20 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.016   0.001   TYR E 190 
 PHE   0.009   0.001   PHE B 215 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.002   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9242)
  covalent geometry    : angle       0.59474 (12531)
  SS BOND              : bond        0.00146 (    3)
  SS BOND              : angle       0.44824 (    6)
  hydrogen bonds       : bond        0.04066 (  413)
  hydrogen bonds       : angle       4.24628 ( 1147)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A   77 MET cc_start: 0.7771 (mtt) cc_final: 0.7314 (mtt)
REVERT: A  166 ILE cc_start: 0.7851 (mm) cc_final: 0.7579 (mt)
REVERT: A  188 LEU cc_start: 0.4765 (mt) cc_final: 0.4164 (pt)
REVERT: C   45 MET cc_start: 0.8813 (mtt) cc_final: 0.8265 (mtt)
REVERT: C   46 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7465 (ttp80)
REVERT: C  217 MET cc_start: 0.8268 (mpp) cc_final: 0.8017 (pmm)
REVERT: C  219 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7350 (mtt-85)
REVERT: E   72 ASP cc_start: 0.7654 (t0) cc_final: 0.7197 (t0)
REVERT: E   86 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7709 (mtt90)
REVERT: E  139 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8593 (m)
  outliers start: 16
  outliers final: 14
  residues processed: 123
  average time/residue: 0.0926
  time to fit residues: 15.8979
Evaluate side-chains
  124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 TYR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  299 CYS
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  284 LEU
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  139 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 64 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.176558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129474 restraints weight = 23185.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 4.10
r_work: 0.3345 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9246  Z= 0.157
  Angle     :  0.625  13.214  12537  Z= 0.321
  Chirality :  0.045   0.294   1430
  Planarity :  0.004   0.055   1565
  Dihedral  :  8.302 115.283   1480
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.29 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.26), residues: 1121
  helix:  2.24 (0.27), residues: 376
  sheet: -1.49 (0.32), residues: 264
  loop : -2.17 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 100 
 TYR   0.022   0.002   TYR E 190 
 PHE   0.012   0.001   PHE C 241 
 TRP   0.013   0.001   TRP E  46 
 HIS   0.004   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 9242)
  covalent geometry    : angle       0.62509 (12531)
  SS BOND              : bond        0.00185 (    3)
  SS BOND              : angle       0.47214 (    6)
  hydrogen bonds       : bond        0.04427 (  413)
  hydrogen bonds       : angle       4.29399 ( 1147)
  Misc. bond           : bond        0.00029 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2617.36 seconds
wall clock time: 45 minutes 31.48 seconds (2731.48 seconds total)