Starting phenix.real_space_refine
on Fri Aug 22 17:49:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xmr_33302/08_2025/7xmr_33302.map"
  }
  resolution = 3.1
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4250      2.51       5
     N    1091      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  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: 6611
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2165
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 90
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "A"
      Number of atoms: 1728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1728
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2351
          Classifications: {'peptide': 314}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 308}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 253
          Classifications: {'peptide': 34}
          Link IDs: {'PTRANS': 4, 'TRANS': 29}
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 114
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU A 234 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 234 " occ=0.00
    residue:
      pdb=" N   ALA A 235 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 235 " occ=0.00
    residue:
      pdb=" N   GLU A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 236 " occ=0.00
    residue:
      pdb=" N   ASP A 237 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ASP A 237 " occ=0.00
    residue:
      pdb=" N   GLU A 238 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 238 " occ=0.00
    residue:
      pdb=" N   GLU A 239 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 239 " occ=0.00
    residue:
      pdb=" N   MET A 240 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  MET A 240 " occ=0.00
  Time building chain proxies: 1.62, per 1000 atoms: 0.25
  Number of scatterers: 6611
  At special positions: 0
  Unit cell: (111.815, 114.95, 80.465, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1218      8.00
     N    1091      7.00
     C    4250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   3 " - pdb=" SG  CYS L  14 " 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: 0.57
  Conformation dependent library (CDL) restraints added in 417.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1640

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      43.2% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'R' and resid 39 through 70
      removed outlier: 3.507A  pdb=" N   ASN R  43 " --> pdb=" O   ASP R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 95
    Processing helix  chain 'R' and resid 95 through 105
      removed outlier: 3.539A  pdb=" N   LEU R 105 " --> pdb=" O   MET R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 146
    Processing helix  chain 'R' and resid 149 through 154
    Processing helix  chain 'R' and resid 155 through 173
    Processing helix  chain 'R' and resid 174 through 180
    Processing helix  chain 'R' and resid 203 through 217
      removed outlier: 3.625A  pdb=" N   LEU R 215 " --> pdb=" O   TYR R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 243
    Processing helix  chain 'R' and resid 246 through 282
      removed outlier: 3.796A  pdb=" N   SER R 250 " --> pdb=" O   LYS R 246 " (cutoff:3.500A)
      Proline residue:  R 271  - end of helix
      removed outlier: 3.560A  pdb=" N   MET R 282 " --> pdb=" O   SER R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 315
      Proline residue:  R 309  - end of helix
      removed outlier: 3.590A  pdb=" N   LEU R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 323
      removed outlier: 3.531A  pdb=" N   LYS R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 33
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.856A  pdb=" N   LYS A  51 " --> pdb=" O   CYS A  47 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.593A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.650A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.765A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 47 through 52
      removed outlier: 3.980A  pdb=" N   LEU C  51 " --> pdb=" O   GLU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 185
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.507A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.297A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.182A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.306A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.118A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.891A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190
    Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.723A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.934A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1044 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: 0.82

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2095
        1.34 -     1.46: 1549
        1.46 -     1.58: 3039
        1.58 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 6754
  Sorted by residual:
  bond pdb=" C   ILE B 270 "
       pdb=" O   ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.19e-02 7.06e+03 5.74e-01
  bond pdb=" C   LEU R 270 "
       pdb=" N   PRO R 271 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.008 1.28e-02 6.10e+03 3.65e-01
  bond pdb=" C   GLY B 144 "
       pdb=" O   GLY B 144 "
    ideal  model  delta    sigma   weight residual
    1.230  1.237 -0.007 1.37e-02 5.33e+03 2.99e-01
  bond pdb=" C   ASP C  48 "
       pdb=" N   PRO C  49 "
    ideal  model  delta    sigma   weight residual
    1.335  1.341 -0.006 1.19e-02 7.06e+03 2.95e-01
  bond pdb=" C   LEU R  96 "
       pdb=" O   LEU R  96 "
    ideal  model  delta    sigma   weight residual
    1.238  1.244 -0.007 1.28e-02 6.10e+03 2.67e-01
  ... (remaining 6749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 9023
        1.15 -     2.29: 131
        2.29 -     3.44: 25
        3.44 -     4.58: 7
        4.58 -     5.73: 7
  Bond angle restraints: 9193
  Sorted by residual:
  angle pdb=" CA  LEU R  96 "
        pdb=" C   LEU R  96 "
        pdb=" N   PRO R  97 "
      ideal   model   delta    sigma   weight residual
     118.44  121.60   -3.16 1.59e+00 3.96e-01 3.95e+00
  angle pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
        pdb=" N   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     116.60  119.46   -2.86 1.45e+00 4.76e-01 3.90e+00
  angle pdb=" N   ILE R 210 "
        pdb=" CA  ILE R 210 "
        pdb=" C   ILE R 210 "
      ideal   model   delta    sigma   weight residual
     113.16  110.44    2.72 1.49e+00 4.50e-01 3.33e+00
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     109.34  113.08   -3.74 2.08e+00 2.31e-01 3.23e+00
  angle pdb=" N   LEU R  96 "
        pdb=" CA  LEU R  96 "
        pdb=" C   LEU R  96 "
      ideal   model   delta    sigma   weight residual
     109.81  113.55   -3.74 2.21e+00 2.05e-01 2.87e+00
  ... (remaining 9188 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.17: 3697
       17.17 -    34.35: 212
       34.35 -    51.52: 35
       51.52 -    68.69: 3
       68.69 -    85.87: 3
  Dihedral angle restraints: 3950
    sinusoidal: 1418
      harmonic: 2532
  Sorted by residual:
  dihedral pdb=" CB  CYS L   3 "
           pdb=" SG  CYS L   3 "
           pdb=" SG  CYS L  14 "
           pdb=" CB  CYS L  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.68   44.68     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CB  GLU B 215 "
           pdb=" CG  GLU B 215 "
           pdb=" CD  GLU B 215 "
           pdb=" OE1 GLU B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.87  -85.87     1      3.00e+01 1.11e-03 9.90e+00
  dihedral pdb=" CB  GLU C  42 "
           pdb=" CG  GLU C  42 "
           pdb=" CD  GLU C  42 "
           pdb=" OE1 GLU C  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.81   85.81     1      3.00e+01 1.11e-03 9.89e+00
  ... (remaining 3947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 685
       0.026 -    0.051: 257
       0.051 -    0.077: 81
       0.077 -    0.102: 38
       0.102 -    0.128: 24
  Chirality restraints: 1085
  Sorted by residual:
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1082 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO B 194 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R  96 "    0.016 5.00e-02 4.00e+02   2.39e-02 9.15e-01
        pdb=" N   PRO R  97 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R  97 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R  97 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 155 "    0.015 5.00e-02 4.00e+02   2.24e-02 8.00e-01
        pdb=" N   PRO R 156 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO R 156 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO R 156 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1492
        2.78 -     3.31: 6170
        3.31 -     3.84: 10874
        3.84 -     4.37: 12706
        4.37 -     4.90: 22023
  Nonbonded interactions: 53265
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 277 "
            pdb=" O   LEU B 318 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR B  65 "
            pdb=" O   PRO B 107 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OH  TYR R 205 "
            pdb=" O   ALA L   1 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ARG B  52 "
            pdb=" NZ  LYS B  89 "
     model   vdw
     2.318 3.120
  ... (remaining 53260 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6108
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      :  0.001   0.017   6756  Z= 0.076
  Angle     :  0.400   5.729   9197  Z= 0.231
  Chirality :  0.036   0.128   1085
  Planarity :  0.002   0.028   1148
  Dihedral  : 10.864  85.867   2304
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (0.23), residues: 859
  helix: -2.56 (0.19), residues: 349
  sheet: -1.24 (0.38), residues: 155
  loop : -2.21 (0.29), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 304 
 TYR   0.004   0.000   TYR B 289 
 PHE   0.006   0.000   PHE R  51 
 TRP   0.002   0.000   TRP B  63 
 HIS   0.006   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00128 ( 6754)
  covalent geometry    : angle       0.39961 ( 9193)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       0.36729 (    4)
  hydrogen bonds       : bond        0.22619 (  361)
  hydrogen bonds       : angle       8.30729 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  180 TYR cc_start: 0.7393 (m-80) cc_final: 0.6500 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0808
  time to fit residues: 17.0008
Evaluate side-chains
  119 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
R  43 ASN
R 146 HIS
R 186 ASN
R 276 ASN
R 304 ASN
A  22 ASN
A 331 ASN
A 333 GLN
B  62 HIS
B  88 ASN
B 110 ASN
B 340 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.212685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.178431 restraints weight = 6981.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.4356 rms_B_bonded: 2.21
r_work: 0.4226 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6756  Z= 0.171
  Angle     :  0.596   6.965   9197  Z= 0.312
  Chirality :  0.043   0.142   1085
  Planarity :  0.004   0.054   1148
  Dihedral  :  3.533  24.443    921
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.62 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.21 (0.27), residues: 859
  helix:  0.16 (0.26), residues: 349
  sheet: -1.08 (0.36), residues: 169
  loop : -1.56 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 208 
 TYR   0.015   0.002   TYR R 228 
 PHE   0.013   0.001   PHE R 272 
 TRP   0.010   0.001   TRP B  99 
 HIS   0.009   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6754)
  covalent geometry    : angle       0.59641 ( 9193)
  SS BOND              : bond        0.00635 (    2)
  SS BOND              : angle       0.74702 (    4)
  hydrogen bonds       : bond        0.03861 (  361)
  hydrogen bonds       : angle       4.95035 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6214 (mmt) cc_final: 0.5948 (mmm)
REVERT: R  180 TYR cc_start: 0.8075 (m-80) cc_final: 0.7177 (m-10)
REVERT: R  241 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.7129 (ttp-170)
REVERT: A  349 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7597 (mttt)
  outliers start: 11
  outliers final: 7
  residues processed: 134
  average time/residue: 0.0738
  time to fit residues: 13.1689
Evaluate side-chains
  117 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0370
   chunk 81 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.212695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.178882 restraints weight = 6859.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 2.19
r_work: 0.4221 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.2964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6756  Z= 0.122
  Angle     :  0.532   7.490   9197  Z= 0.277
  Chirality :  0.041   0.155   1085
  Planarity :  0.003   0.040   1148
  Dihedral  :  3.490  23.373    921
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.06 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 859
  helix:  1.10 (0.27), residues: 350
  sheet: -0.89 (0.36), residues: 173
  loop : -1.41 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 208 
 TYR   0.013   0.001   TYR A 296 
 PHE   0.013   0.001   PHE L   6 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6754)
  covalent geometry    : angle       0.53211 ( 9193)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       0.52511 (    4)
  hydrogen bonds       : bond        0.03491 (  361)
  hydrogen bonds       : angle       4.63534 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6193 (mmt) cc_final: 0.5945 (mmm)
REVERT: R  241 ARG cc_start: 0.7371 (ttp-170) cc_final: 0.7141 (ttp-170)
REVERT: A  283 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.5450 (tt)
REVERT: A  349 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7574 (mttt)
REVERT: B  101 MET cc_start: 0.8018 (mtp) cc_final: 0.7771 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 119
  average time/residue: 0.0768
  time to fit residues: 12.3693
Evaluate side-chains
  109 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 331 ASN
** L   5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.204124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.168891 restraints weight = 7005.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.4279 rms_B_bonded: 2.22
r_work: 0.4143 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6756  Z= 0.153
  Angle     :  0.569   7.225   9197  Z= 0.295
  Chirality :  0.042   0.175   1085
  Planarity :  0.003   0.038   1148
  Dihedral  :  3.744  20.393    921
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.36 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.28), residues: 859
  helix:  1.42 (0.28), residues: 350
  sheet: -0.59 (0.37), residues: 167
  loop : -1.23 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.013   0.001   TYR A 296 
 PHE   0.011   0.001   PHE R 272 
 TRP   0.026   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6754)
  covalent geometry    : angle       0.56925 ( 9193)
  SS BOND              : bond        0.00643 (    2)
  SS BOND              : angle       0.63218 (    4)
  hydrogen bonds       : bond        0.03599 (  361)
  hydrogen bonds       : angle       4.65968 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6199 (mmt) cc_final: 0.5945 (mmm)
REVERT: A  283 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6132 (tt)
REVERT: A  349 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7624 (mttt)
REVERT: B  258 ASP cc_start: 0.4375 (t0) cc_final: 0.4088 (t70)
REVERT: B  329 THR cc_start: 0.8714 (m) cc_final: 0.8237 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 128
  average time/residue: 0.0719
  time to fit residues: 12.2151
Evaluate side-chains
  124 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 43 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0370
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.202074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.167885 restraints weight = 7133.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 2.15
r_work: 0.4116 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3959 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6756  Z= 0.139
  Angle     :  0.554   7.500   9197  Z= 0.289
  Chirality :  0.042   0.148   1085
  Planarity :  0.004   0.045   1148
  Dihedral  :  3.796  21.239    921
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.79 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.29), residues: 859
  helix:  1.62 (0.28), residues: 349
  sheet: -0.60 (0.37), residues: 169
  loop : -1.22 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 208 
 TYR   0.019   0.002   TYR A 296 
 PHE   0.013   0.001   PHE R 272 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6754)
  covalent geometry    : angle       0.55372 ( 9193)
  SS BOND              : bond        0.00568 (    2)
  SS BOND              : angle       0.63383 (    4)
  hydrogen bonds       : bond        0.03519 (  361)
  hydrogen bonds       : angle       4.69902 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6167 (mmt) cc_final: 0.5914 (mmm)
REVERT: A  296 TYR cc_start: 0.7548 (t80) cc_final: 0.7227 (t80)
REVERT: A  349 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7668 (mttt)
REVERT: B  101 MET cc_start: 0.8405 (mtp) cc_final: 0.8155 (mtp)
REVERT: B  329 THR cc_start: 0.8797 (m) cc_final: 0.8385 (p)
  outliers start: 21
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0729
  time to fit residues: 12.7281
Evaluate side-chains
  125 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
A 188 HIS
A 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.202331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.167416 restraints weight = 7027.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 2.21
r_work: 0.4097 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.140
  Angle     :  0.559   7.345   9197  Z= 0.291
  Chirality :  0.042   0.161   1085
  Planarity :  0.004   0.050   1148
  Dihedral  :  3.831  22.797    921
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.51 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.29), residues: 859
  helix:  1.74 (0.28), residues: 348
  sheet: -0.69 (0.36), residues: 179
  loop : -1.03 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.015   0.002   TYR B  59 
 PHE   0.014   0.001   PHE R 272 
 TRP   0.024   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6754)
  covalent geometry    : angle       0.55846 ( 9193)
  SS BOND              : bond        0.00606 (    2)
  SS BOND              : angle       0.68594 (    4)
  hydrogen bonds       : bond        0.03471 (  361)
  hydrogen bonds       : angle       4.68067 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6147 (mmt) cc_final: 0.5910 (mmm)
REVERT: A  182 THR cc_start: 0.6684 (m) cc_final: 0.6349 (t)
REVERT: A  255 ASN cc_start: 0.5285 (OUTLIER) cc_final: 0.4012 (p0)
REVERT: A  349 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7616 (mttt)
REVERT: B  101 MET cc_start: 0.8273 (mtp) cc_final: 0.8013 (mtp)
REVERT: B  329 THR cc_start: 0.8762 (m) cc_final: 0.8348 (p)
  outliers start: 22
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0954
  time to fit residues: 16.2093
Evaluate side-chains
  125 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  241 ARG
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  255 ASN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0170
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.7018

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
R 276 ASN
A 255 ASN
A 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.202139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.167943 restraints weight = 6986.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 2.14
r_work: 0.4121 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3964 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6756  Z= 0.144
  Angle     :  0.568   7.292   9197  Z= 0.294
  Chirality :  0.043   0.235   1085
  Planarity :  0.004   0.054   1148
  Dihedral  :  3.875  21.856    921
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.23 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.29), residues: 859
  helix:  1.62 (0.28), residues: 354
  sheet: -0.66 (0.36), residues: 179
  loop : -0.96 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 208 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.029   0.001   PHE A 189 
 TRP   0.023   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6754)
  covalent geometry    : angle       0.56838 ( 9193)
  SS BOND              : bond        0.00592 (    2)
  SS BOND              : angle       0.69941 (    4)
  hydrogen bonds       : bond        0.03499 (  361)
  hydrogen bonds       : angle       4.70572 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6088 (mmt) cc_final: 0.5851 (mmm)
REVERT: A  182 THR cc_start: 0.6850 (m) cc_final: 0.6378 (t)
REVERT: A  198 MET cc_start: 0.8360 (mpp) cc_final: 0.8138 (mpp)
REVERT: A  349 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7640 (mttt)
REVERT: B  101 MET cc_start: 0.8406 (mtp) cc_final: 0.8131 (mtm)
REVERT: B  329 THR cc_start: 0.8759 (m) cc_final: 0.8406 (p)
  outliers start: 24
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0886
  time to fit residues: 14.7479
Evaluate side-chains
  126 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  241 ARG
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 76 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
A 255 ASN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.198990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.164337 restraints weight = 7021.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 2.18
r_work: 0.4117 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6756  Z= 0.142
  Angle     :  0.583   7.501   9197  Z= 0.302
  Chirality :  0.043   0.238   1085
  Planarity :  0.004   0.061   1148
  Dihedral  :  3.906  21.638    921
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.51 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.27 (0.29), residues: 859
  helix:  1.72 (0.28), residues: 347
  sheet: -0.70 (0.36), residues: 179
  loop : -0.92 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.040   0.001   PHE R 272 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6754)
  covalent geometry    : angle       0.58290 ( 9193)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       0.70081 (    4)
  hydrogen bonds       : bond        0.03521 (  361)
  hydrogen bonds       : angle       4.77158 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.258 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6093 (mmt) cc_final: 0.5867 (mmm)
REVERT: A  182 THR cc_start: 0.6779 (m) cc_final: 0.6434 (t)
REVERT: A  198 MET cc_start: 0.8156 (mpp) cc_final: 0.7937 (mpp)
REVERT: A  349 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7600 (mttt)
REVERT: B  101 MET cc_start: 0.8405 (mtp) cc_final: 0.8105 (mtm)
REVERT: B  329 THR cc_start: 0.8744 (m) cc_final: 0.8415 (p)
REVERT: C   46 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6495 (mmtt)
  outliers start: 20
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0925
  time to fit residues: 15.2287
Evaluate side-chains
  126 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
R 276 ASN
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.198144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.163930 restraints weight = 7108.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4209 rms_B_bonded: 2.12
r_work: 0.4080 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3924 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6756  Z= 0.159
  Angle     :  0.597   7.732   9197  Z= 0.310
  Chirality :  0.044   0.242   1085
  Planarity :  0.004   0.064   1148
  Dihedral  :  3.980  21.201    921
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.37 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.29), residues: 859
  helix:  1.61 (0.28), residues: 349
  sheet: -0.81 (0.36), residues: 181
  loop : -0.93 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.037   0.001   PHE R 272 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6754)
  covalent geometry    : angle       0.59687 ( 9193)
  SS BOND              : bond        0.00645 (    2)
  SS BOND              : angle       0.73433 (    4)
  hydrogen bonds       : bond        0.03619 (  361)
  hydrogen bonds       : angle       4.80706 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.212 
Fit side-chains
REVERT: R  101 MET cc_start: 0.6168 (mmt) cc_final: 0.5912 (mmm)
REVERT: A  182 THR cc_start: 0.6924 (m) cc_final: 0.6499 (t)
REVERT: A  198 MET cc_start: 0.8341 (mpp) cc_final: 0.8122 (mpp)
REVERT: A  308 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: A  349 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7675 (mttt)
REVERT: B  329 THR cc_start: 0.8775 (m) cc_final: 0.8485 (p)
  outliers start: 23
  outliers final: 21
  residues processed: 123
  average time/residue: 0.0947
  time to fit residues: 15.1312
Evaluate side-chains
  124 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  214 ILE
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0980
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5600

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.198727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.164122 restraints weight = 6979.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 2.17
r_work: 0.4146 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6756  Z= 0.136
  Angle     :  0.583   7.661   9197  Z= 0.302
  Chirality :  0.043   0.231   1085
  Planarity :  0.004   0.063   1148
  Dihedral  :  3.948  21.505    921
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.37 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.22 (0.29), residues: 859
  helix:  1.65 (0.28), residues: 349
  sheet: -0.79 (0.35), residues: 181
  loop : -0.88 (0.36), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.036   0.001   PHE R 272 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6754)
  covalent geometry    : angle       0.58262 ( 9193)
  SS BOND              : bond        0.00566 (    2)
  SS BOND              : angle       0.70504 (    4)
  hydrogen bonds       : bond        0.03563 (  361)
  hydrogen bonds       : angle       4.76022 ( 1044)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 MET cc_start: 0.6129 (mmt) cc_final: 0.5901 (mmm)
REVERT: A   33 GLU cc_start: 0.7686 (tt0) cc_final: 0.7423 (tt0)
REVERT: A  182 THR cc_start: 0.6849 (m) cc_final: 0.6517 (t)
REVERT: A  208 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7207 (ttp-110)
REVERT: A  349 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7791 (mttt)
REVERT: B  329 THR cc_start: 0.8723 (m) cc_final: 0.8446 (p)
  outliers start: 21
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0865
  time to fit residues: 14.2633
Evaluate side-chains
  127 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  121 VAL
Chi-restraints excluded: chain R residue  153 TRP
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  304 ASN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  325 CYS
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain L residue    6 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 80 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
R 276 ASN
** R 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.198456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.163870 restraints weight = 6953.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 2.15
r_work: 0.4055 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6756  Z= 0.157
  Angle     :  0.599   7.709   9197  Z= 0.311
  Chirality :  0.044   0.235   1085
  Planarity :  0.004   0.062   1148
  Dihedral  :  4.005  20.902    921
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.23 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.29), residues: 859
  helix:  1.56 (0.28), residues: 351
  sheet: -0.83 (0.35), residues: 184
  loop : -0.88 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 208 
 TYR   0.017   0.002   TYR B  59 
 PHE   0.033   0.001   PHE R 272 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6754)
  covalent geometry    : angle       0.59896 ( 9193)
  SS BOND              : bond        0.00652 (    2)
  SS BOND              : angle       0.74520 (    4)
  hydrogen bonds       : bond        0.03663 (  361)
  hydrogen bonds       : angle       4.82196 ( 1044)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2165.52 seconds
wall clock time: 37 minutes 41.49 seconds (2261.49 seconds total)