Starting phenix.real_space_refine
on Sun Aug 24 02:58:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tmd_41385/08_2025/8tmd_41385.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.046
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Mg      3      5.21       5
     S      57      5.16       5
     C   10406      2.51       5
     N    2605      2.21       5
     O    2940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16011
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 803
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 983
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
    Chain: "A"
      Number of atoms: 2797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2797
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 13, 'TRANS': 320}
    Chain: "B"
      Number of atoms: 2900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2900
          Classifications: {'peptide': 348}
          Link IDs: {'PTRANS': 15, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 2797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2797
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 13, 'TRANS': 320}
    Chain: "D"
      Number of atoms: 2838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2838
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 15, 'TRANS': 324}
    Chain: "E"
      Number of atoms: 2890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 347, 2890
          Classifications: {'peptide': 347}
          Link IDs: {'PTRANS': 15, 'TRANS': 331}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.29, per 1000 atoms: 0.27
  Number of scatterers: 16011
  At special positions: 0
  Unit cell: (120.684, 144.18, 138.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     Mg      3     11.99
     O    2940      8.00
     N    2605      7.00
     C   10406      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 685.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3716

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 12 sheets defined
      53.1% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.528A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 3.528A  pdb=" N   SER A  49 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A  51 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      Proline residue:  A  52  - end of helix
      removed outlier: 3.535A  pdb=" N   ASP A  55 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 3.768A  pdb=" N   VAL A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 147 through 156
    Processing helix  chain 'A' and resid 165 through 201
      removed outlier: 3.513A  pdb=" N   LEU A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 238
      Proline residue:  A 227  - end of helix
      removed outlier: 3.975A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 281
    Processing helix  chain 'A' and resid 282 through 300
      removed outlier: 3.765A  pdb=" N   LYS A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 312
    Processing helix  chain 'A' and resid 326 through 347
      removed outlier: 3.649A  pdb=" N   VAL A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
      removed outlier: 3.531A  pdb=" N   PHE B  53 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 81
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 117 through 120
      removed outlier: 3.552A  pdb=" N   HIS B 120 " --> pdb=" O   LYS B 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 117 through 120'
    Processing helix  chain 'B' and resid 147 through 156
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 165 through 202
      removed outlier: 3.611A  pdb=" N   LEU B 169 " --> pdb=" O   ARG B 165 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   GLU B 201 " --> pdb=" O   GLU B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 238
      Proline residue:  B 227  - end of helix
    Processing helix  chain 'B' and resid 247 through 312
      Proline residue:  B 303  - end of helix
    Processing helix  chain 'B' and resid 326 through 348
    Processing helix  chain 'C' and resid 69 through 80
      removed outlier: 4.434A  pdb=" N   VAL C  73 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 91
      removed outlier: 3.605A  pdb=" N   LEU C  91 " --> pdb=" O   LEU C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 157
    Processing helix  chain 'C' and resid 166 through 202
      removed outlier: 3.627A  pdb=" N   LEU C 170 " --> pdb=" O   ALA C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 236
      removed outlier: 4.112A  pdb=" N   VAL C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLN C 209 " --> pdb=" O   LYS C 205 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TRP C 226 " --> pdb=" O   ARG C 222 " (cutoff:3.500A)
      Proline residue:  C 227  - end of helix
    Processing helix  chain 'C' and resid 244 through 246
      No H-bonds generated for 'chain 'C' and resid 244 through 246'
    Processing helix  chain 'C' and resid 247 through 312
      removed outlier: 3.651A  pdb=" N   LEU C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP C 277 " --> pdb=" O   SER C 273 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
    Processing helix  chain 'C' and resid 325 through 348
    Processing helix  chain 'D' and resid 46 through 51
      removed outlier: 3.823A  pdb=" N   VAL D  50 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 4.186A  pdb=" N   VAL D  73 " --> pdb=" O   ARG D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'D' and resid 147 through 157
    Processing helix  chain 'D' and resid 160 through 164
      removed outlier: 3.615A  pdb=" N   LYS D 163 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 202
      removed outlier: 3.714A  pdb=" N   LEU D 169 " --> pdb=" O   ARG D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 238
      removed outlier: 4.211A  pdb=" N   GLN D 209 " --> pdb=" O   LYS D 205 " (cutoff:3.500A)
      Proline residue:  D 227  - end of helix
    Processing helix  chain 'D' and resid 244 through 246
      No H-bonds generated for 'chain 'D' and resid 244 through 246'
    Processing helix  chain 'D' and resid 247 through 311
      removed outlier: 3.672A  pdb=" N   PHE D 251 " --> pdb=" O   THR D 247 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASP D 277 " --> pdb=" O   SER D 273 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 326 through 348
      removed outlier: 4.253A  pdb=" N   VAL D 330 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU D 331 " --> pdb=" O   TYR D 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
      removed outlier: 3.512A  pdb=" N   SER E  49 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU E  51 " --> pdb=" O   GLU E  48 " (cutoff:3.500A)
      Proline residue:  E  52  - end of helix
      removed outlier: 3.576A  pdb=" N   ASP E  55 " --> pdb=" O   PRO E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 81
      removed outlier: 3.792A  pdb=" N   VAL E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 83 through 92
    Processing helix  chain 'E' and resid 147 through 156
    Processing helix  chain 'E' and resid 165 through 202
      removed outlier: 3.545A  pdb=" N   LEU E 169 " --> pdb=" O   ARG E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 238
      Proline residue:  E 227  - end of helix
      removed outlier: 3.785A  pdb=" N   GLU E 230 " --> pdb=" O   TRP E 226 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ASP E 238 " --> pdb=" O   SER E 234 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 244 through 246
      No H-bonds generated for 'chain 'E' and resid 244 through 246'
    Processing helix  chain 'E' and resid 247 through 311
      removed outlier: 4.197A  pdb=" N   LEU E 276 " --> pdb=" O   VAL E 272 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ASP E 277 " --> pdb=" O   SER E 273 " (cutoff:3.500A)
      Proline residue:  E 303  - end of helix
      removed outlier: 3.572A  pdb=" N   TYR E 311 " --> pdb=" O   ILE E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 325 through 348
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AA2, first strand: chain 'L' and resid 13 through 14
    Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.522A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 90 through 91
      removed outlier: 3.523A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.865A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 15
      removed outlier: 6.560A  pdb=" N   CYS H  99 " --> pdb=" O   TRP H 119 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   TRP H 119 " --> pdb=" O   CYS H  99 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ARG H 101 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 44
      removed outlier: 6.390A  pdb=" N   THR A  60 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   MET A 138 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ILE A  62 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 44
    Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 41
      removed outlier: 3.544A  pdb=" N   GLU C  28 " --> pdb=" O   THR C  65 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   THR C  60 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
      removed outlier: 7.912A  pdb=" N   MET C 138 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   ILE C  62 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44
      removed outlier: 6.652A  pdb=" N   THR D  60 " --> pdb=" O   VAL D 136 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   MET D 138 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ILE D  62 " --> pdb=" O   MET D 138 " (cutoff:3.500A)
      removed outlier: 7.834A  pdb=" N   GLN D 140 " --> pdb=" O   ILE D  62 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ILE D  64 " --> pdb=" O   GLN D 140 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 39 through 44
      removed outlier: 3.520A  pdb=" N   ASN E  33 " --> pdb=" O   ARG E  40 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TRP E  61 " --> pdb=" O   MET E  32 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLU E 121 " --> pdb=" O   ASP E 116 " (cutoff:3.500A)

    1003 hydrogen bonds defined for protein.
    2892 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: 2.94

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5040
        1.34 -     1.46: 3539
        1.46 -     1.58: 7691
        1.58 -     1.70: 0
        1.70 -     1.82: 105
  Bond restraints: 16375
  Sorted by residual:
  bond pdb=" CG1 ILE A  90 "
       pdb=" CD1 ILE A  90 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.92e+00
  bond pdb=" SD  MET E 291 "
       pdb=" CE  MET E 291 "
    ideal  model  delta    sigma   weight residual
    1.791  1.763  0.028 2.50e-02 1.60e+03 1.24e+00
  bond pdb=" CB  VAL E 254 "
       pdb=" CG2 VAL E 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.23e+00
  bond pdb=" CG1 ILE D  67 "
       pdb=" CD1 ILE D  67 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.21e+00
  bond pdb=" CD1 TYR E 171 "
       pdb=" CE1 TYR E 171 "
    ideal  model  delta    sigma   weight residual
    1.382  1.349  0.033 3.00e-02 1.11e+03 1.21e+00
  ... (remaining 16370 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 21650
        1.62 -     3.24: 453
        3.24 -     4.85: 84
        4.85 -     6.47: 17
        6.47 -     8.09: 6
  Bond angle restraints: 22210
  Sorted by residual:
  angle pdb=" C   LEU E 235 "
        pdb=" N   TYR E 236 "
        pdb=" CA  TYR E 236 "
      ideal   model   delta    sigma   weight residual
     122.09  114.28    7.81 1.79e+00 3.12e-01 1.90e+01
  angle pdb=" C   LEU A 235 "
        pdb=" N   TYR A 236 "
        pdb=" CA  TYR A 236 "
      ideal   model   delta    sigma   weight residual
     121.52  114.59    6.93 1.84e+00 2.95e-01 1.42e+01
  angle pdb=" C   LEU B 235 "
        pdb=" N   TYR B 236 "
        pdb=" CA  TYR B 236 "
      ideal   model   delta    sigma   weight residual
     121.66  115.76    5.90 1.76e+00 3.23e-01 1.12e+01
  angle pdb=" C   GLU C  48 "
        pdb=" CA  GLU C  48 "
        pdb=" CB  GLU C  48 "
      ideal   model   delta    sigma   weight residual
     110.42  116.84   -6.42 1.99e+00 2.53e-01 1.04e+01
  angle pdb=" CA  ARG B 237 "
        pdb=" CB  ARG B 237 "
        pdb=" CG  ARG B 237 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.30e+00
  ... (remaining 22205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 8864
       17.70 -    35.40: 809
       35.40 -    53.09: 118
       53.09 -    70.79: 25
       70.79 -    88.49: 19
  Dihedral angle restraints: 9835
    sinusoidal: 4086
      harmonic: 5749
  Sorted by residual:
  dihedral pdb=" CB  CYS L  24 "
           pdb=" SG  CYS L  24 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  149.30  -56.30     1      1.00e+01 1.00e-02 4.27e+01
  dihedral pdb=" CA  ARG B 237 "
           pdb=" C   ARG B 237 "
           pdb=" N   ASP B 238 "
           pdb=" CA  ASP B 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ILE E 300 "
           pdb=" C   ILE E 300 "
           pdb=" N   PHE E 301 "
           pdb=" CA  PHE E 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.80  -20.20     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 9832 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1952
       0.049 -    0.097: 457
       0.097 -    0.146: 114
       0.146 -    0.194: 1
       0.194 -    0.243: 2
  Chirality restraints: 2526
  Sorted by residual:
  chirality pdb=" CB  ILE D  67 "
            pdb=" CA  ILE D  67 "
            pdb=" CG1 ILE D  67 "
            pdb=" CG2 ILE D  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  TRP E 226 "
            pdb=" N   TRP E 226 "
            pdb=" C   TRP E 226 "
            pdb=" CB  TRP E 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE B 307 "
            pdb=" CA  ILE B 307 "
            pdb=" CG1 ILE B 307 "
            pdb=" CG2 ILE B 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 2523 not shown)

  Planarity restraints: 2778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 237 "   -0.202 9.50e-02 1.11e+02   9.15e-02 6.99e+00
        pdb=" NE  ARG B 237 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 237 "   -0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 237 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 237 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 240 "   -0.043 5.00e-02 4.00e+02   6.52e-02 6.79e+00
        pdb=" N   PRO A 241 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 241 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 241 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 148 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO C 149 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C 149 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C 149 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2775 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 148
        2.64 -     3.21: 14561
        3.21 -     3.77: 24780
        3.77 -     4.34: 34115
        4.34 -     4.90: 56004
  Nonbonded interactions: 129608
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 115 "
            pdb=" OE1 GLU E 191 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" OD1 ASN B 288 "
            pdb=" OG1 THR C 287 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" OD1 ASN A 285 "
            pdb=" OH  TYR B 279 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" NZ  LYS B   4 "
            pdb=" OE1 GLU B 100 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" OG1 THR D  65 "
            pdb=" O   LYS D 142 "
     model   vdw
     2.180 3.040
  ... (remaining 129603 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 17 through 350)
  selection = (chain 'B' and resid 17 through 350)
  selection = (chain 'C' and resid 17 through 350)
  selection = (chain 'D' and resid 17 through 350)
  selection = (chain 'E' and resid 17 through 350)
}

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=0.49 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:             3.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.260
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  16377  Z= 0.160
  Angle     :  0.604   8.088  22214  Z= 0.319
  Chirality :  0.043   0.243   2526
  Planarity :  0.005   0.091   2778
  Dihedral  : 13.972  88.488   6113
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.33 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.20), residues: 1924
  helix:  2.31 (0.16), residues: 965
  sheet:  0.78 (0.28), residues: 376
  loop : -1.35 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG B 237 
 TYR   0.033   0.002   TYR E 236 
 PHE   0.024   0.001   PHE A 306 
 TRP   0.012   0.001   TRP E 323 
 HIS   0.016   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (16375)
  covalent geometry    : angle       0.60308 (22210)
  SS BOND              : bond        0.00027 (    2)
  SS BOND              : angle       2.14800 (    4)
  hydrogen bonds       : bond        0.15058 (  998)
  hydrogen bonds       : angle       6.04994 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 419
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: H   90 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7279 (mtt180)
REVERT: H   96 VAL cc_start: 0.9099 (p) cc_final: 0.8717 (t)
REVERT: A   63 ASN cc_start: 0.6863 (t0) cc_final: 0.6565 (t0)
REVERT: A   96 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6941 (mpt180)
REVERT: B   32 MET cc_start: 0.8780 (mtt) cc_final: 0.8541 (mtt)
REVERT: B  260 GLN cc_start: 0.7700 (mt0) cc_final: 0.7205 (mm-40)
REVERT: D   19 TYR cc_start: 0.6805 (t80) cc_final: 0.6567 (t80)
REVERT: E   10 LYS cc_start: 0.7378 (ptmm) cc_final: 0.7117 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 419
  average time/residue: 0.5187
  time to fit residues: 245.2109
Evaluate side-chains
  343 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 343
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.3980
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  85 GLN
B  92 ASN
B 134 ASN
D 120 HIS
D 157 ASN
E  63 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.197892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.160715 restraints weight = 18212.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.70
r_work: 0.3281 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3252
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3252 r_free = 0.3252    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16377  Z= 0.191
  Angle     :  0.625   8.304  22214  Z= 0.332
  Chirality :  0.044   0.216   2526
  Planarity :  0.005   0.050   2778
  Dihedral  :  4.469  19.879   2149
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.81 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.20), residues: 1924
  helix:  2.24 (0.16), residues: 974
  sheet:  0.81 (0.27), residues: 377
  loop : -1.53 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 229 
 TYR   0.021   0.002   TYR D 327 
 PHE   0.024   0.002   PHE B 301 
 TRP   0.019   0.001   TRP D 226 
 HIS   0.014   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (16375)
  covalent geometry    : angle       0.62488 (22210)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       2.05967 (    4)
  hydrogen bonds       : bond        0.06369 (  998)
  hydrogen bonds       : angle       4.85928 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 356
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: L   19 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6654 (ttm170)
REVERT: H   90 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7332 (mtt180)
REVERT: H   96 VAL cc_start: 0.9208 (p) cc_final: 0.8948 (t)
REVERT: A   96 ARG cc_start: 0.7916 (mmt180) cc_final: 0.7401 (mpt180)
REVERT: A  289 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7633 (mt-10)
REVERT: B   32 MET cc_start: 0.8853 (mtt) cc_final: 0.8626 (mtt)
REVERT: C  291 MET cc_start: 0.7782 (tpp) cc_final: 0.7466 (mmt)
REVERT: D   19 TYR cc_start: 0.6929 (t80) cc_final: 0.6725 (t80)
REVERT: D   32 MET cc_start: 0.7561 (mtm) cc_final: 0.7027 (mtt)
REVERT: D  152 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6395 (mm-30)
REVERT: D  226 TRP cc_start: 0.8197 (m100) cc_final: 0.7888 (m100)
REVERT: D  229 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7679 (ttm-80)
REVERT: D  291 MET cc_start: 0.8375 (tpt) cc_final: 0.8057 (tpt)
REVERT: E   10 LYS cc_start: 0.7483 (ptmm) cc_final: 0.6920 (ptmt)
REVERT: E   35 SER cc_start: 0.7532 (t) cc_final: 0.6846 (p)
REVERT: E   42 PHE cc_start: 0.6339 (t80) cc_final: 0.6011 (t80)
REVERT: E  205 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7033 (mtmm)
REVERT: E  210 ARG cc_start: 0.8355 (mtp180) cc_final: 0.7498 (mtm-85)
REVERT: E  229 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8279 (mtm180)
  outliers start: 51
  outliers final: 30
  residues processed: 381
  average time/residue: 0.4975
  time to fit residues: 215.4858
Evaluate side-chains
  364 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 330
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain A residue  135 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  313 MET
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  229 ARG
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 162 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 177 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
A  95 GLN
D 120 HIS
D 157 ASN
E  63 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.197674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.161595 restraints weight = 18365.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.95
r_work: 0.3298 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  16377  Z= 0.184
  Angle     :  0.604   8.786  22214  Z= 0.319
  Chirality :  0.044   0.198   2526
  Planarity :  0.005   0.048   2778
  Dihedral  :  4.471  19.338   2149
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.25 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.20), residues: 1924
  helix:  2.22 (0.16), residues: 975
  sheet:  0.80 (0.26), residues: 383
  loop : -1.62 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 202 
 TYR   0.018   0.002   TYR H 106 
 PHE   0.022   0.002   PHE A  27 
 TRP   0.016   0.001   TRP E 226 
 HIS   0.011   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (16375)
  covalent geometry    : angle       0.60370 (22210)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       1.49803 (    4)
  hydrogen bonds       : bond        0.06266 (  998)
  hydrogen bonds       : angle       4.70282 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 358
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   19 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6585 (ttm170)
REVERT: L   90 GLN cc_start: 0.8485 (tt0) cc_final: 0.8191 (tt0)
REVERT: H   90 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7275 (mtt180)
REVERT: H   96 VAL cc_start: 0.9188 (p) cc_final: 0.8908 (t)
REVERT: A  269 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7352 (mtt-85)
REVERT: A  289 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7534 (mt-10)
REVERT: B  230 GLU cc_start: 0.8482 (tp30) cc_final: 0.8261 (mm-30)
REVERT: B  286 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7788 (mppt)
REVERT: C  291 MET cc_start: 0.7809 (tpp) cc_final: 0.7453 (mmt)
REVERT: D   32 MET cc_start: 0.7651 (mtm) cc_final: 0.7028 (ttt)
REVERT: D  121 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6640 (tm-30)
REVERT: D  152 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6401 (mm-30)
REVERT: D  226 TRP cc_start: 0.8207 (m100) cc_final: 0.7836 (m100)
REVERT: D  230 GLU cc_start: 0.7641 (tp30) cc_final: 0.7357 (tp30)
REVERT: D  291 MET cc_start: 0.8341 (tpt) cc_final: 0.7874 (tpt)
REVERT: E   10 LYS cc_start: 0.7455 (ptmm) cc_final: 0.6887 (ptmt)
REVERT: E   35 SER cc_start: 0.7515 (t) cc_final: 0.6851 (p)
REVERT: E   42 PHE cc_start: 0.6373 (t80) cc_final: 0.6116 (t80)
REVERT: E  116 ASP cc_start: 0.6897 (t70) cc_final: 0.6601 (t0)
REVERT: E  205 LYS cc_start: 0.7518 (ttmm) cc_final: 0.6831 (mtmm)
REVERT: E  210 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7445 (mtm-85)
REVERT: E  229 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8272 (mtm180)
  outliers start: 62
  outliers final: 35
  residues processed: 383
  average time/residue: 0.4835
  time to fit residues: 210.3316
Evaluate side-chains
  383 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 343
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  229 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 168 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 138 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 148 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 123 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
B 288 ASN
D 120 HIS
D 126 GLN
D 157 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.197580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.160673 restraints weight = 18290.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 3.71
r_work: 0.3309 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16377  Z= 0.163
  Angle     :  0.583   9.319  22214  Z= 0.307
  Chirality :  0.043   0.329   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.417  18.424   2149
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.64 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.20), residues: 1924
  helix:  2.31 (0.16), residues: 968
  sheet:  0.73 (0.26), residues: 370
  loop : -1.57 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 202 
 TYR   0.019   0.002   TYR D 327 
 PHE   0.021   0.002   PHE A  27 
 TRP   0.018   0.001   TRP E 226 
 HIS   0.009   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (16375)
  covalent geometry    : angle       0.58301 (22210)
  SS BOND              : bond        0.00090 (    2)
  SS BOND              : angle       1.10704 (    4)
  hydrogen bonds       : bond        0.05994 (  998)
  hydrogen bonds       : angle       4.57418 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 356
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   19 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6602 (ttm170)
REVERT: L   38 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8766 (tt0)
REVERT: L   90 GLN cc_start: 0.8501 (tt0) cc_final: 0.8255 (tt0)
REVERT: H   96 VAL cc_start: 0.9166 (p) cc_final: 0.8904 (t)
REVERT: A  269 ARG cc_start: 0.7611 (mtp180) cc_final: 0.7236 (mtt-85)
REVERT: A  289 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7427 (mt-10)
REVERT: B  286 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7763 (mppt)
REVERT: C  253 ASP cc_start: 0.6395 (t0) cc_final: 0.6176 (t0)
REVERT: C  297 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7646 (tt)
REVERT: D   32 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7058 (ttt)
REVERT: D  121 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6554 (tm-30)
REVERT: D  152 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6413 (mm-30)
REVERT: D  226 TRP cc_start: 0.8164 (m100) cc_final: 0.7757 (m100)
REVERT: D  230 GLU cc_start: 0.7544 (tp30) cc_final: 0.7207 (tp30)
REVERT: D  341 MET cc_start: 0.6999 (mmm) cc_final: 0.6733 (mmp)
REVERT: E   10 LYS cc_start: 0.7522 (ptmm) cc_final: 0.6872 (ptmt)
REVERT: E   12 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7667 (mm)
REVERT: E   35 SER cc_start: 0.7555 (t) cc_final: 0.6884 (p)
REVERT: E   42 PHE cc_start: 0.6301 (t80) cc_final: 0.6050 (t80)
REVERT: E  116 ASP cc_start: 0.6836 (t70) cc_final: 0.6511 (t0)
REVERT: E  163 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7431 (ttmm)
REVERT: E  205 LYS cc_start: 0.7431 (ttmm) cc_final: 0.6750 (mtmm)
  outliers start: 70
  outliers final: 43
  residues processed: 391
  average time/residue: 0.4333
  time to fit residues: 192.0488
Evaluate side-chains
  392 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 340
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 ARG
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 133 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0870
   chunk 80 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 92 optimal weight:    0.2980
   chunk 134 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 120 HIS
D 126 GLN
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 140 GLN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.200182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.161741 restraints weight = 18169.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 3.21
r_work: 0.3285 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16377  Z= 0.154
  Angle     :  0.573  11.618  22214  Z= 0.301
  Chirality :  0.043   0.327   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.390  18.568   2149
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.69 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.20), residues: 1924
  helix:  2.36 (0.16), residues: 969
  sheet:  0.72 (0.26), residues: 372
  loop : -1.55 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 237 
 TYR   0.020   0.001   TYR D  19 
 PHE   0.024   0.002   PHE B  39 
 TRP   0.017   0.001   TRP E 226 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (16375)
  covalent geometry    : angle       0.57245 (22210)
  SS BOND              : bond        0.00043 (    2)
  SS BOND              : angle       0.95523 (    4)
  hydrogen bonds       : bond        0.05816 (  998)
  hydrogen bonds       : angle       4.51184 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 352
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8758 (tt0)
REVERT: L   90 GLN cc_start: 0.8478 (tt0) cc_final: 0.8270 (tt0)
REVERT: H   96 VAL cc_start: 0.9228 (p) cc_final: 0.8916 (t)
REVERT: A  269 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7261 (mtt-85)
REVERT: A  289 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: C  297 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: D   32 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7142 (ttt)
REVERT: D   85 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7930 (tp)
REVERT: D  121 GLU cc_start: 0.6875 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: D  152 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6412 (mm-30)
REVERT: D  226 TRP cc_start: 0.8212 (m100) cc_final: 0.7798 (m100)
REVERT: E   10 LYS cc_start: 0.7451 (ptmm) cc_final: 0.6766 (ptmt)
REVERT: E   12 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7687 (mm)
REVERT: E   35 SER cc_start: 0.7581 (t) cc_final: 0.6882 (p)
REVERT: E   42 PHE cc_start: 0.6346 (t80) cc_final: 0.6120 (t80)
REVERT: E  116 ASP cc_start: 0.6850 (t70) cc_final: 0.6506 (t0)
REVERT: E  205 LYS cc_start: 0.7415 (ttmm) cc_final: 0.6744 (mtmm)
  outliers start: 76
  outliers final: 50
  residues processed: 396
  average time/residue: 0.4718
  time to fit residues: 212.5955
Evaluate side-chains
  395 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 338
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  114 ASN
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  142 LYS
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   85 LEU
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  138 MET
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 122 optimal weight:    0.0040
   chunk 59 optimal weight:    0.3980
   chunk 163 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 173 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   chunk 164 optimal weight:    2.9990
   chunk 162 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
B 288 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.199986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.161852 restraints weight = 18193.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.17
r_work: 0.3289 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16377  Z= 0.158
  Angle     :  0.580  10.083  22214  Z= 0.303
  Chirality :  0.043   0.369   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.398  18.532   2149
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.74 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.20), residues: 1924
  helix:  2.36 (0.16), residues: 968
  sheet:  0.73 (0.26), residues: 377
  loop : -1.56 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  25 
 TYR   0.026   0.002   TYR D  19 
 PHE   0.025   0.002   PHE A  27 
 TRP   0.016   0.001   TRP E 226 
 HIS   0.008   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (16375)
  covalent geometry    : angle       0.57972 (22210)
  SS BOND              : bond        0.00367 (    2)
  SS BOND              : angle       1.17616 (    4)
  hydrogen bonds       : bond        0.05831 (  998)
  hydrogen bonds       : angle       4.47173 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 344
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8766 (tt0)
REVERT: L   90 GLN cc_start: 0.8455 (tt0) cc_final: 0.8204 (tt0)
REVERT: H   96 VAL cc_start: 0.9207 (p) cc_final: 0.8890 (t)
REVERT: A  269 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7146 (mtt-85)
REVERT: A  289 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7567 (mt-10)
REVERT: B  100 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7847 (mm-30)
REVERT: B  177 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7977 (tt)
REVERT: B  286 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7817 (mppt)
REVERT: C  297 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7692 (tt)
REVERT: D   32 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7188 (ttt)
REVERT: D  121 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6531 (tm-30)
REVERT: D  152 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6377 (mm-30)
REVERT: D  186 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7552 (tp30)
REVERT: D  226 TRP cc_start: 0.8244 (m100) cc_final: 0.7808 (m100)
REVERT: E   10 LYS cc_start: 0.7454 (ptmm) cc_final: 0.6851 (ptmt)
REVERT: E   12 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7553 (mm)
REVERT: E   35 SER cc_start: 0.7598 (t) cc_final: 0.6898 (p)
REVERT: E  205 LYS cc_start: 0.7386 (ttmm) cc_final: 0.6720 (mtmm)
  outliers start: 78
  outliers final: 47
  residues processed: 385
  average time/residue: 0.4862
  time to fit residues: 212.7039
Evaluate side-chains
  397 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 341
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  142 LYS
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  145 ASP
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 161 optimal weight:    0.3980
   chunk 66 optimal weight:    0.4980
   chunk 109 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0970
   chunk 183 optimal weight:    1.9990
   chunk 156 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0370
   chunk 50 optimal weight:    1.9990
   chunk 163 optimal weight:    1.9990
   chunk 187 optimal weight:    0.9980
   chunk 185 optimal weight:    0.5980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
B 288 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.199937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.160973 restraints weight = 18155.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.04
r_work: 0.3295 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16377  Z= 0.137
  Angle     :  0.559   9.182  22214  Z= 0.292
  Chirality :  0.042   0.331   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.311  18.324   2149
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.91 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.20), residues: 1924
  helix:  2.47 (0.16), residues: 969
  sheet:  0.63 (0.27), residues: 365
  loop : -1.48 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  25 
 TYR   0.025   0.001   TYR D  19 
 PHE   0.026   0.001   PHE A  27 
 TRP   0.015   0.001   TRP E 226 
 HIS   0.005   0.000   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16375)
  covalent geometry    : angle       0.55851 (22210)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       0.80072 (    4)
  hydrogen bonds       : bond        0.05494 (  998)
  hydrogen bonds       : angle       4.38706 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 344
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8732 (tt0)
REVERT: H   96 VAL cc_start: 0.9199 (p) cc_final: 0.8896 (t)
REVERT: A  116 ASP cc_start: 0.6891 (t70) cc_final: 0.6595 (t0)
REVERT: A  269 ARG cc_start: 0.7546 (mtp180) cc_final: 0.7130 (mtt-85)
REVERT: A  289 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7522 (mt-10)
REVERT: B  177 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7970 (tt)
REVERT: B  238 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7629 (m-30)
REVERT: B  286 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7807 (mppt)
REVERT: D   32 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7158 (ttt)
REVERT: D  121 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6550 (tm-30)
REVERT: D  152 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6384 (mm-30)
REVERT: D  186 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7403 (tp30)
REVERT: D  226 TRP cc_start: 0.8220 (m100) cc_final: 0.7758 (m100)
REVERT: E   10 LYS cc_start: 0.7458 (ptmm) cc_final: 0.6779 (ptmt)
REVERT: E   12 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7573 (mm)
REVERT: E   35 SER cc_start: 0.7605 (t) cc_final: 0.6904 (p)
REVERT: E  116 ASP cc_start: 0.6857 (t70) cc_final: 0.6509 (t0)
REVERT: E  163 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7579 (ttmt)
REVERT: E  205 LYS cc_start: 0.7355 (ttmm) cc_final: 0.6722 (mtmm)
  outliers start: 70
  outliers final: 43
  residues processed: 380
  average time/residue: 0.4671
  time to fit residues: 201.7499
Evaluate side-chains
  383 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 330
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  142 LYS
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  270 ASP
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 154 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 158 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0470
   chunk 42 optimal weight:    0.7980
   chunk 169 optimal weight:    0.5980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 ASN
** D  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 120 HIS
** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.198491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.161330 restraints weight = 18277.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.61
r_work: 0.3297 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16377  Z= 0.159
  Angle     :  0.586  11.146  22214  Z= 0.305
  Chirality :  0.043   0.303   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.339  18.764   2149
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.58 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.20), residues: 1924
  helix:  2.39 (0.16), residues: 968
  sheet:  0.61 (0.26), residues: 372
  loop : -1.54 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  25 
 TYR   0.027   0.002   TYR D  19 
 PHE   0.027   0.002   PHE A  27 
 TRP   0.019   0.001   TRP E 226 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (16375)
  covalent geometry    : angle       0.58629 (22210)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       1.18276 (    4)
  hydrogen bonds       : bond        0.05687 (  998)
  hydrogen bonds       : angle       4.41521 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 343
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8721 (tt0)
REVERT: H   96 VAL cc_start: 0.9216 (p) cc_final: 0.8887 (t)
REVERT: A  116 ASP cc_start: 0.6961 (t70) cc_final: 0.6678 (t0)
REVERT: A  269 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7209 (mtt-85)
REVERT: A  289 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7489 (mt-10)
REVERT: B  193 ASP cc_start: 0.7557 (t70) cc_final: 0.7352 (t0)
REVERT: B  238 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7581 (m-30)
REVERT: B  286 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7903 (mppt)
REVERT: D   32 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7235 (ttt)
REVERT: D  121 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6574 (tm-30)
REVERT: D  152 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6449 (mm-30)
REVERT: D  186 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7534 (tp30)
REVERT: D  226 TRP cc_start: 0.8297 (m100) cc_final: 0.7869 (m100)
REVERT: D  341 MET cc_start: 0.6843 (mmm) cc_final: 0.6576 (mmp)
REVERT: E   10 LYS cc_start: 0.7500 (ptmm) cc_final: 0.6844 (ptmt)
REVERT: E   12 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7632 (mm)
REVERT: E   35 SER cc_start: 0.7678 (t) cc_final: 0.7008 (p)
REVERT: E  116 ASP cc_start: 0.6918 (t70) cc_final: 0.6557 (t0)
REVERT: E  163 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7621 (ttmt)
REVERT: E  205 LYS cc_start: 0.7447 (ttmm) cc_final: 0.6820 (mtmm)
  outliers start: 69
  outliers final: 50
  residues processed: 382
  average time/residue: 0.4540
  time to fit residues: 196.9609
Evaluate side-chains
  399 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 340
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  142 LYS
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  145 ASP
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 1 optimal weight:    0.0770
   chunk 54 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 115 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
A 140 GLN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 ASN
D 120 HIS
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.200089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.163187 restraints weight = 18139.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 3.11
r_work: 0.3323 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16377  Z= 0.162
  Angle     :  0.596  10.380  22214  Z= 0.308
  Chirality :  0.043   0.296   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.381  23.716   2149
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.13 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.20), residues: 1924
  helix:  2.38 (0.16), residues: 969
  sheet:  0.61 (0.26), residues: 376
  loop : -1.53 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  25 
 TYR   0.029   0.002   TYR D  19 
 PHE   0.029   0.002   PHE A  27 
 TRP   0.017   0.001   TRP E 226 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (16375)
  covalent geometry    : angle       0.59537 (22210)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       1.29167 (    4)
  hydrogen bonds       : bond        0.05751 (  998)
  hydrogen bonds       : angle       4.42870 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  415 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 345
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8732 (tt0)
REVERT: H   96 VAL cc_start: 0.9216 (p) cc_final: 0.8889 (t)
REVERT: A   41 GLU cc_start: 0.6907 (mp0) cc_final: 0.6529 (mp0)
REVERT: A  116 ASP cc_start: 0.6805 (t70) cc_final: 0.6567 (t0)
REVERT: A  269 ARG cc_start: 0.7508 (mtp180) cc_final: 0.7137 (mtt-85)
REVERT: A  289 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7460 (mt-10)
REVERT: B  193 ASP cc_start: 0.7438 (t70) cc_final: 0.7182 (t0)
REVERT: B  238 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7439 (m-30)
REVERT: B  286 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7840 (mppt)
REVERT: C  138 MET cc_start: 0.3882 (pmm) cc_final: 0.3113 (pp-130)
REVERT: C  297 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7712 (tt)
REVERT: D   32 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7205 (ttt)
REVERT: D  121 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6615 (tm-30)
REVERT: D  152 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6362 (mm-30)
REVERT: D  186 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7428 (tp30)
REVERT: D  226 TRP cc_start: 0.8240 (m100) cc_final: 0.7828 (m100)
REVERT: E   10 LYS cc_start: 0.7454 (ptmm) cc_final: 0.6811 (ptmt)
REVERT: E   12 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7609 (mm)
REVERT: E   35 SER cc_start: 0.7648 (t) cc_final: 0.6983 (p)
REVERT: E  116 ASP cc_start: 0.6871 (t0) cc_final: 0.6516 (t0)
REVERT: E  163 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7609 (ttmt)
REVERT: E  205 LYS cc_start: 0.7374 (ttmm) cc_final: 0.6747 (mtmm)
  outliers start: 70
  outliers final: 49
  residues processed: 382
  average time/residue: 0.4280
  time to fit residues: 186.2832
Evaluate side-chains
  395 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 336
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  289 GLU
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  187 LYS
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  145 ASP
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain E residue  177 LEU
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 171 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 170 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 103 optimal weight:    5.9990
   chunk 168 optimal weight:    0.0270
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 288 ASN
D 120 HIS
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.199348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.162498 restraints weight = 18320.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.59
r_work: 0.3311 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3276
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3276 r_free = 0.3276    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3276
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16377  Z= 0.144
  Angle     :  0.585  10.225  22214  Z= 0.303
  Chirality :  0.043   0.286   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.339  24.784   2149
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.57 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.20), residues: 1924
  helix:  2.42 (0.16), residues: 968
  sheet:  0.61 (0.27), residues: 369
  loop : -1.49 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  25 
 TYR   0.029   0.002   TYR D  19 
 PHE   0.031   0.002   PHE B  39 
 TRP   0.021   0.001   TRP E 226 
 HIS   0.006   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (16375)
  covalent geometry    : angle       0.58477 (22210)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.94621 (    4)
  hydrogen bonds       : bond        0.05550 (  998)
  hydrogen bonds       : angle       4.38901 ( 2892)

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

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

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3848 Ramachandran restraints generated.
    1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 342
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   38 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8710 (tt0)
REVERT: H   96 VAL cc_start: 0.9218 (p) cc_final: 0.8901 (t)
REVERT: A   41 GLU cc_start: 0.6871 (mp0) cc_final: 0.6574 (mp0)
REVERT: A  116 ASP cc_start: 0.6871 (t70) cc_final: 0.6668 (t0)
REVERT: A  269 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7160 (mtt-85)
REVERT: A  337 ILE cc_start: 0.6577 (tt) cc_final: 0.6332 (OUTLIER)
REVERT: B  193 ASP cc_start: 0.7489 (t70) cc_final: 0.7219 (t0)
REVERT: B  238 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7446 (m-30)
REVERT: B  286 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7874 (mppt)
REVERT: C  297 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7698 (tt)
REVERT: D   27 PHE cc_start: 0.5850 (t80) cc_final: 0.5573 (t80)
REVERT: D   32 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7180 (ttt)
REVERT: D  121 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6647 (tm-30)
REVERT: D  152 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6432 (mm-30)
REVERT: D  186 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7563 (tp30)
REVERT: D  226 TRP cc_start: 0.8281 (m100) cc_final: 0.7866 (m100)
REVERT: E   10 LYS cc_start: 0.7468 (ptmm) cc_final: 0.6875 (ptmt)
REVERT: E   12 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7651 (mm)
REVERT: E   35 SER cc_start: 0.7649 (t) cc_final: 0.7058 (p)
REVERT: E  116 ASP cc_start: 0.6968 (t0) cc_final: 0.6584 (t0)
REVERT: E  163 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7649 (ttmt)
REVERT: E  180 ASP cc_start: 0.7604 (t0) cc_final: 0.7391 (t0)
REVERT: E  205 LYS cc_start: 0.7472 (ttmm) cc_final: 0.6879 (mtmm)
  outliers start: 64
  outliers final: 50
  residues processed: 377
  average time/residue: 0.4378
  time to fit residues: 188.0067
Evaluate side-chains
  393 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 336
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   32 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue   74 SER
Chi-restraints excluded: chain H residue   86 MET
Chi-restraints excluded: chain H residue  117 ASP
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  175 ASP
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  167 ASP
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  286 LYS
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  297 ILE
Chi-restraints excluded: chain C residue  318 MET
Chi-restraints excluded: chain D residue   32 MET
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   73 VAL
Chi-restraints excluded: chain D residue  128 SER
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain D residue  152 GLU
Chi-restraints excluded: chain D residue  186 GLU
Chi-restraints excluded: chain D residue  234 SER
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain D residue  289 GLU
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain E residue   12 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue   56 SER
Chi-restraints excluded: chain E residue  114 THR
Chi-restraints excluded: chain E residue  218 LEU
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain E residue  263 ASP
Chi-restraints excluded: chain E residue  282 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 157 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 113 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 156 optimal weight:    0.4980
   chunk 155 optimal weight:    0.6980
   chunk 174 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 160 optimal weight:    0.0170
   chunk 18 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** B  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 120 HIS
D 157 ASN
E 288 ASN
E 314 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.198546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.162154 restraints weight = 18140.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.42
r_work: 0.3339 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16377  Z= 0.163
  Angle     :  0.603   9.889  22214  Z= 0.313
  Chirality :  0.043   0.283   2526
  Planarity :  0.004   0.046   2778
  Dihedral  :  4.378  24.874   2149
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 22.91 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.28 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.20), residues: 1924
  helix:  2.36 (0.16), residues: 968
  sheet:  0.61 (0.26), residues: 380
  loop : -1.58 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG L  25 
 TYR   0.028   0.002   TYR D  19 
 PHE   0.029   0.002   PHE A  27 
 TRP   0.019   0.001   TRP E 226 
 HIS   0.007   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (16375)
  covalent geometry    : angle       0.60323 (22210)
  SS BOND              : bond        0.00106 (    2)
  SS BOND              : angle       1.23169 (    4)
  hydrogen bonds       : bond        0.05739 (  998)
  hydrogen bonds       : angle       4.42663 ( 2892)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6080.03 seconds
wall clock time: 104 minutes 24.74 seconds (6264.74 seconds total)