Starting phenix.real_space_refine
on Tue Mar 11 22:59:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bkk_44643/03_2025/9bkk_44643_neut.cif"
  }
  resolution = 2.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.100
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      56      5.16       5
     C    4362      2.51       5
     N    1156      2.21       5
     O    1235      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6809
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1599
          Classifications: {'peptide': 203}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 3, 'TRANS': 199}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 2497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2497
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 92
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 407
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "P"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 77
          Classifications: {'peptide': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2228
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 4.52, per 1000 atoms: 0.66
  Number of scatterers: 6809
  At special positions: 0
  Unit cell: (84.15, 90.1, 126.65, 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      56     16.00
     O    1235      8.00
     N    1156      7.00
     C    4362      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 196 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 931.4 milliseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      47.8% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 39
      removed outlier: 3.569A  pdb=" N   ASN A  29 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS A  36 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.905A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.666A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.742A  pdb=" N   ARG A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 25
      removed outlier: 3.531A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 39 through 69
    Processing helix  chain 'R' and resid 74 through 105
      Proline residue:  R  96  - end of helix
      Proline residue:  R 101  - end of helix
    Processing helix  chain 'R' and resid 110 through 145
      removed outlier: 3.575A  pdb=" N   VAL R 133 " --> pdb=" O   THR R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 152
    Processing helix  chain 'R' and resid 154 through 173
    Processing helix  chain 'R' and resid 174 through 179
      removed outlier: 3.762A  pdb=" N   ILE R 178 " --> pdb=" O   THR R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 202 through 217
    Processing helix  chain 'R' and resid 218 through 238
      removed outlier: 3.828A  pdb=" N   MET R 225 " --> pdb=" O   PRO R 221 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR R 229 " --> pdb=" O   MET R 225 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 348
      removed outlier: 3.671A  pdb=" N   MET R 314 " --> pdb=" O   ARG R 310 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE R 323 " --> pdb=" O   VAL R 319 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
      removed outlier: 8.237A  pdb=" N   ALA R 341 " --> pdb=" O   ALA R 337 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   SER R 342 " --> pdb=" O   TYR R 338 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 349 through 371
      removed outlier: 3.877A  pdb=" N   SER R 353 " --> pdb=" O   GLY R 349 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE R 354 " --> pdb=" O   THR R 350 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   SER R 363 " --> pdb=" O   SER R 359 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   CYS R 364 " --> pdb=" O   TYR R 360 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 374 through 385
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 9.749A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.567A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.595A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.598A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.900A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.659A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.521A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.370A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.816A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 183 through 186

    400 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.86

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1198
        1.32 -     1.44: 1778
        1.44 -     1.57: 3886
        1.57 -     1.69: 1
        1.69 -     1.82: 82
  Bond restraints: 6945
  Sorted by residual:
  bond pdb=" C   MET R 327 "
       pdb=" O   MET R 327 "
    ideal  model  delta    sigma   weight residual
    1.241  1.194  0.047 9.80e-03 1.04e+04 2.29e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.595  0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" N   VAL B 158 "
       pdb=" CA  VAL B 158 "
    ideal  model  delta    sigma   weight residual
    1.459  1.511 -0.052 1.26e-02 6.30e+03 1.69e+01
  bond pdb=" N   VAL R 183 "
       pdb=" CA  VAL R 183 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 9.00e-03 1.23e+04 1.66e+01
  bond pdb=" N   ILE B 157 "
       pdb=" CA  ILE B 157 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.19e-02 7.06e+03 1.33e+01
  ... (remaining 6940 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6507
        1.71 -     3.43: 2434
        3.43 -     5.14: 433
        5.14 -     6.85: 58
        6.85 -     8.56: 8
  Bond angle restraints: 9440
  Sorted by residual:
  angle pdb=" CA  ASP A 347 "
        pdb=" CB  ASP A 347 "
        pdb=" CG  ASP A 347 "
      ideal   model   delta    sigma   weight residual
     112.60  120.10   -7.50 1.00e+00 1.00e+00 5.63e+01
  angle pdb=" CA  PHE B 151 "
        pdb=" CB  PHE B 151 "
        pdb=" CG  PHE B 151 "
      ideal   model   delta    sigma   weight residual
     113.80  120.73   -6.93 1.00e+00 1.00e+00 4.80e+01
  angle pdb=" N   LEU B 152 "
        pdb=" CA  LEU B 152 "
        pdb=" C   LEU B 152 "
      ideal   model   delta    sigma   weight residual
     113.12  104.89    8.23 1.25e+00 6.40e-01 4.34e+01
  angle pdb=" N   LYS B 301 "
        pdb=" CA  LYS B 301 "
        pdb=" C   LYS B 301 "
      ideal   model   delta    sigma   weight residual
     113.72  105.47    8.25 1.30e+00 5.92e-01 4.03e+01
  angle pdb=" CA  PHE B 292 "
        pdb=" CB  PHE B 292 "
        pdb=" CG  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     113.80  119.76   -5.96 1.00e+00 1.00e+00 3.55e+01
  ... (remaining 9435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.83: 3696
       13.83 -    27.66: 314
       27.66 -    41.48: 66
       41.48 -    55.31: 20
       55.31 -    69.14: 13
  Dihedral angle restraints: 4109
    sinusoidal: 1506
      harmonic: 2603
  Sorted by residual:
  dihedral pdb=" C   ASP A 347 "
           pdb=" N   ASP A 347 "
           pdb=" CA  ASP A 347 "
           pdb=" CB  ASP A 347 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.47   14.87     0      2.50e+00 1.60e-01 3.54e+01
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.30   29.70     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" C   LYS A 293 "
           pdb=" N   LYS A 293 "
           pdb=" CA  LYS A 293 "
           pdb=" CB  LYS A 293 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.92   14.32     0      2.50e+00 1.60e-01 3.28e+01
  ... (remaining 4106 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 808
       0.101 -    0.202: 270
       0.202 -    0.303: 24
       0.303 -    0.404: 7
       0.404 -    0.505: 3
  Chirality restraints: 1112
  Sorted by residual:
  chirality pdb=" CA  ASP A 347 "
            pdb=" N   ASP A 347 "
            pdb=" C   ASP A 347 "
            pdb=" CB  ASP A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.37e+00
  chirality pdb=" CB  THR B 321 "
            pdb=" CA  THR B 321 "
            pdb=" OG1 THR B 321 "
            pdb=" CG2 THR B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.05    0.50 2.00e-01 2.50e+01 6.33e+00
  chirality pdb=" CA  LYS A 293 "
            pdb=" N   LYS A 293 "
            pdb=" C   LYS A 293 "
            pdb=" CB  LYS A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.70e+00
  ... (remaining 1109 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 277 "   -0.134 2.00e-02 2.50e+03   7.00e-02 1.23e+02
        pdb=" CG  TRP A 277 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 277 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 277 "    0.069 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 277 "    0.041 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 277 "    0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 277 "    0.102 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 277 "   -0.071 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 277 "    0.022 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 277 "   -0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 332 "   -0.093 2.00e-02 2.50e+03   4.97e-02 6.18e+01
        pdb=" CG  TRP B 332 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 332 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 332 "    0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 332 "    0.030 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 332 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 332 "    0.064 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 332 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 332 "    0.028 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 332 "   -0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "    0.075 2.00e-02 2.50e+03   4.45e-02 4.95e+01
        pdb=" CG  TRP A 281 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "   -0.066 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.019 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "    0.057 2.00e-02 2.50e+03
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2442
        2.89 -     3.39: 6643
        3.39 -     3.90: 11499
        3.90 -     4.40: 13396
        4.40 -     4.90: 22504
  Nonbonded interactions: 56484
  Sorted by model distance:
  nonbonded pdb=" O   TRP P   5 "
            pdb=" NH1 ARG R 336 "
     model   vdw
     2.388 3.120
  nonbonded pdb=" O   MET A  25 "
            pdb=" ND2 ASN A  29 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.431 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.456 3.040
  nonbonded pdb=" O   THR R  74 "
            pdb=" N   ASN R  77 "
     model   vdw
     2.470 3.120
  ... (remaining 56479 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.330
  Find NCS groups from input model:        0.060
  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:11.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5877
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      :  0.012   0.084   6945  Z= 0.795
  Angle     :  1.754   8.564   9440  Z= 1.211
  Chirality :  0.097   0.505   1112
  Planarity :  0.012   0.100   1183
  Dihedral  : 12.285  69.136   2408
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  :  4.49 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  5.07 %
    Favored  : 92.39 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.26), residues: 868
  helix: -1.29 (0.23), residues: 384
  sheet:  1.39 (0.48), residues: 108
  loop : -1.57 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.134   0.019   TRP A 277 
 HIS   0.016   0.004   HIS B 225 
 PHE   0.052   0.008   PHE B 278 
 TYR   0.086   0.012   TYR R 176 
 ARG   0.007   0.001   ARG B 314 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LYS cc_start: 0.6626 (mtmm) cc_final: 0.6390 (mttt)
REVERT: A  211 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6752 (mttt)
REVERT: A  280 ARG cc_start: 0.6407 (ttp-110) cc_final: 0.6043 (ttt-90)
REVERT: A  338 LYS cc_start: 0.5288 (mtpt) cc_final: 0.5070 (mttt)
REVERT: A  371 ASN cc_start: 0.6838 (m-40) cc_final: 0.6278 (m-40)
REVERT: A  386 MET cc_start: 0.6013 (ttp) cc_final: 0.5640 (ptp)
REVERT: B   59 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6182 (m-80)
REVERT: B  277 SER cc_start: 0.7346 (t) cc_final: 0.6991 (m)
REVERT: R   69 ASN cc_start: 0.5960 (t0) cc_final: 0.5413 (m-40)
REVERT: R  148 GLN cc_start: 0.6204 (mp10) cc_final: 0.5799 (mm-40)
REVERT: R  160 LYS cc_start: 0.4549 (mmtp) cc_final: 0.4236 (tmtt)
REVERT: R  194 ASN cc_start: 0.6196 (m-40) cc_final: 0.5955 (m-40)
REVERT: R  217 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6391 (tt)
REVERT: R  225 MET cc_start: 0.7046 (mtp) cc_final: 0.6846 (mtm)
REVERT: R  235 GLU cc_start: 0.5738 (mm-30) cc_final: 0.5183 (tt0)
REVERT: R  310 ARG cc_start: 0.5341 (ttm-80) cc_final: 0.5069 (ptm-80)
REVERT: R  344 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6559 (mt-10)
REVERT: R  348 SER cc_start: 0.6946 (t) cc_final: 0.6497 (m)
  outliers start: 18
  outliers final: 2
  residues processed: 197
  average time/residue: 1.1277
  time to fit residues: 233.8554
Evaluate side-chains
  125 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 121
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain R residue  217 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 36 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 267 GLN
B  88 ASN
G  18 GLN
R 333 ASN
R 366 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.205854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.161161 restraints weight = 7050.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 2.13
r_work: 0.3921 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3795 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6945  Z= 0.256
  Angle     :  0.693  10.256   9440  Z= 0.369
  Chirality :  0.047   0.162   1112
  Planarity :  0.005   0.067   1183
  Dihedral  :  6.495  72.028    957
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.51 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.28), residues: 868
  helix:  1.16 (0.26), residues: 389
  sheet:  0.15 (0.38), residues: 188
  loop : -0.81 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 169 
 HIS   0.010   0.002   HIS A 220 
 PHE   0.018   0.002   PHE B 292 
 TYR   0.021   0.002   TYR R 176 
 ARG   0.007   0.001   ARG A 283 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 THR cc_start: 0.7823 (p) cc_final: 0.7521 (t)
REVERT: A  211 LYS cc_start: 0.7423 (mtpt) cc_final: 0.7094 (mmtt)
REVERT: A  271 ASN cc_start: 0.6000 (m-40) cc_final: 0.5611 (m-40)
REVERT: A  274 LYS cc_start: 0.6720 (tttt) cc_final: 0.6345 (ttmp)
REVERT: A  280 ARG cc_start: 0.6879 (ttp-110) cc_final: 0.6645 (ttt-90)
REVERT: A  343 LYS cc_start: 0.7607 (tmtt) cc_final: 0.7375 (tmmt)
REVERT: A  371 ASN cc_start: 0.7568 (m-40) cc_final: 0.7279 (m-40)
REVERT: A  386 MET cc_start: 0.6925 (ttp) cc_final: 0.6683 (ptp)
REVERT: R   45 ILE cc_start: 0.5678 (pt) cc_final: 0.5258 (mt)
REVERT: R   69 ASN cc_start: 0.6383 (t0) cc_final: 0.5373 (m-40)
REVERT: R  160 LYS cc_start: 0.5673 (mmtp) cc_final: 0.5223 (tmtt)
REVERT: R  194 ASN cc_start: 0.6555 (m-40) cc_final: 0.6283 (m-40)
REVERT: R  202 ASN cc_start: 0.5615 (p0) cc_final: 0.5275 (p0)
  outliers start: 27
  outliers final: 9
  residues processed: 142
  average time/residue: 1.1867
  time to fit residues: 177.4731
Evaluate side-chains
  107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  233 SER
Chi-restraints excluded: chain R residue  306 MET
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  359 SER
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0030
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 254 ASN
B  75 GLN
B 259 GLN
G  18 GLN
R 131 ASN
R 210 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.206197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.161891 restraints weight = 7154.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 2.11
r_work: 0.3933 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6945  Z= 0.161
  Angle     :  0.568   8.926   9440  Z= 0.301
  Chirality :  0.043   0.260   1112
  Planarity :  0.004   0.051   1183
  Dihedral  :  5.366  68.660    952
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.21 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 868
  helix:  1.99 (0.26), residues: 388
  sheet:  0.24 (0.37), residues: 185
  loop : -0.56 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.012   0.002   PHE B 199 
 TYR   0.010   0.001   TYR R 176 
 ARG   0.005   0.000   ARG A 342 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.7331 (mtpt) cc_final: 0.7120 (mmtt)
REVERT: A  271 ASN cc_start: 0.6017 (m-40) cc_final: 0.5549 (m-40)
REVERT: A  274 LYS cc_start: 0.6741 (tttt) cc_final: 0.6373 (ttmp)
REVERT: A  280 ARG cc_start: 0.6885 (ttp-110) cc_final: 0.6621 (ttp80)
REVERT: A  343 LYS cc_start: 0.7708 (tmtt) cc_final: 0.7459 (tmmt)
REVERT: A  371 ASN cc_start: 0.7529 (m-40) cc_final: 0.7250 (m-40)
REVERT: B  217 MET cc_start: 0.7078 (ptt) cc_final: 0.6857 (pp-130)
REVERT: R   45 ILE cc_start: 0.5834 (pt) cc_final: 0.5415 (mt)
REVERT: R  148 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7006 (mm-40)
REVERT: R  160 LYS cc_start: 0.5810 (mmtp) cc_final: 0.5391 (tmtt)
REVERT: R  194 ASN cc_start: 0.6290 (m-40) cc_final: 0.6074 (m-40)
REVERT: R  233 SER cc_start: 0.7017 (OUTLIER) cc_final: 0.6607 (m)
REVERT: R  235 GLU cc_start: 0.6333 (mm-30) cc_final: 0.5794 (tt0)
  outliers start: 22
  outliers final: 8
  residues processed: 126
  average time/residue: 1.2788
  time to fit residues: 169.4900
Evaluate side-chains
  109 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  148 GLN
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  233 SER
Chi-restraints excluded: chain R residue  306 MET
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0870
   chunk 78 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    2.2164

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 254 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.198788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.152770 restraints weight = 7119.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.13
r_work: 0.3838 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3709 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.4528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6945  Z= 0.292
  Angle     :  0.669  10.610   9440  Z= 0.352
  Chirality :  0.047   0.151   1112
  Planarity :  0.005   0.045   1183
  Dihedral  :  5.907  78.988    952
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 16.48 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.28), residues: 868
  helix:  1.50 (0.26), residues: 391
  sheet:  0.09 (0.37), residues: 177
  loop : -0.76 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 211 
 HIS   0.009   0.002   HIS B 266 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.022   0.002   TYR R 176 
 ARG   0.006   0.001   ARG R 378 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.7424 (mtpt) cc_final: 0.7051 (mmtt)
REVERT: A  271 ASN cc_start: 0.6304 (m-40) cc_final: 0.5707 (m-40)
REVERT: A  274 LYS cc_start: 0.6904 (tttt) cc_final: 0.6563 (ttmp)
REVERT: A  280 ARG cc_start: 0.7066 (ttp-110) cc_final: 0.6752 (ttp80)
REVERT: A  343 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7719 (ttpt)
REVERT: B  215 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6257 (mt-10)
REVERT: G   19 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5961 (mm)
REVERT: R   45 ILE cc_start: 0.5857 (pt) cc_final: 0.5535 (mt)
REVERT: R  160 LYS cc_start: 0.5948 (mmtp) cc_final: 0.5534 (tmtt)
REVERT: R  194 ASN cc_start: 0.6524 (m-40) cc_final: 0.6323 (m-40)
REVERT: R  233 SER cc_start: 0.7184 (OUTLIER) cc_final: 0.6822 (m)
REVERT: R  235 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6043 (tt0)
REVERT: R  306 MET cc_start: 0.3802 (OUTLIER) cc_final: 0.3290 (pp-130)
REVERT: R  346 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.5666 (tmt170)
  outliers start: 34
  outliers final: 15
  residues processed: 124
  average time/residue: 1.2829
  time to fit residues: 166.9879
Evaluate side-chains
  114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  233 SER
Chi-restraints excluded: chain R residue  306 MET
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  359 SER
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 374 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.200991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.155798 restraints weight = 7041.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 2.10
r_work: 0.3875 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3746 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6945  Z= 0.193
  Angle     :  0.566   6.632   9440  Z= 0.298
  Chirality :  0.043   0.141   1112
  Planarity :  0.004   0.041   1183
  Dihedral  :  5.544  77.079    952
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.75 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.28), residues: 868
  helix:  1.92 (0.26), residues: 388
  sheet:  0.01 (0.36), residues: 187
  loop : -0.66 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.011   0.001   TYR R 338 
 ARG   0.005   0.001   ARG R  73 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6679 (mt)
REVERT: A  211 LYS cc_start: 0.7465 (mtpt) cc_final: 0.7224 (mmtt)
REVERT: A  271 ASN cc_start: 0.6225 (m-40) cc_final: 0.5646 (m-40)
REVERT: A  274 LYS cc_start: 0.6850 (tttt) cc_final: 0.6496 (ttmp)
REVERT: A  343 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7644 (tmmt)
REVERT: A  371 ASN cc_start: 0.7571 (m-40) cc_final: 0.7259 (m-40)
REVERT: B   19 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7606 (mtp-110)
REVERT: B  219 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7527 (mmt90)
REVERT: B  226 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6270 (mp0)
REVERT: G   19 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6208 (mm)
REVERT: R   45 ILE cc_start: 0.5854 (pt) cc_final: 0.5550 (mt)
REVERT: R  160 LYS cc_start: 0.6002 (mmtp) cc_final: 0.5651 (tmtt)
REVERT: R  194 ASN cc_start: 0.6524 (m-40) cc_final: 0.6269 (m-40)
REVERT: R  233 SER cc_start: 0.7085 (OUTLIER) cc_final: 0.6746 (m)
REVERT: R  235 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6045 (tt0)
REVERT: R  338 TYR cc_start: 0.6918 (m-80) cc_final: 0.6587 (m-80)
REVERT: R  346 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5813 (tpm170)
  outliers start: 27
  outliers final: 10
  residues processed: 124
  average time/residue: 1.2345
  time to fit residues: 160.9150
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue  114 CYS
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  233 SER
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.202024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.157136 restraints weight = 7094.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 2.10
r_work: 0.3887 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6945  Z= 0.170
  Angle     :  0.538   5.970   9440  Z= 0.286
  Chirality :  0.042   0.135   1112
  Planarity :  0.004   0.040   1183
  Dihedral  :  5.409  76.122    952
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.15 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 868
  helix:  2.16 (0.26), residues: 386
  sheet:  0.04 (0.35), residues: 188
  loop : -0.59 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.020   0.002   PHE R  93 
 TYR   0.023   0.001   TYR R 179 
 ARG   0.006   0.000   ARG R  73 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6737 (mt)
REVERT: A  271 ASN cc_start: 0.6243 (m-40) cc_final: 0.5660 (m-40)
REVERT: A  274 LYS cc_start: 0.6867 (tttt) cc_final: 0.6524 (ttmp)
REVERT: A  343 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7689 (ttpt)
REVERT: A  371 ASN cc_start: 0.7565 (m-40) cc_final: 0.7248 (m-40)
REVERT: B   19 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7624 (mtp-110)
REVERT: B  215 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5868 (mt-10)
REVERT: B  217 MET cc_start: 0.7187 (ptt) cc_final: 0.5804 (pmt)
REVERT: B  226 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6230 (mp0)
REVERT: R   45 ILE cc_start: 0.5847 (pt) cc_final: 0.5559 (mt)
REVERT: R  160 LYS cc_start: 0.5998 (mmtp) cc_final: 0.5681 (tmtt)
REVERT: R  194 ASN cc_start: 0.6330 (m-40) cc_final: 0.6098 (m-40)
REVERT: R  235 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6109 (tt0)
REVERT: R  314 MET cc_start: 0.6359 (tpp) cc_final: 0.6139 (tpp)
REVERT: R  338 TYR cc_start: 0.7067 (m-80) cc_final: 0.6728 (m-80)
REVERT: R  346 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5790 (tpm170)
  outliers start: 21
  outliers final: 9
  residues processed: 117
  average time/residue: 1.1932
  time to fit residues: 146.8825
Evaluate side-chains
  113 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain P residue    3 MET
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.202377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.157785 restraints weight = 7105.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 2.10
r_work: 0.3898 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3766 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6945  Z= 0.162
  Angle     :  0.535   6.414   9440  Z= 0.285
  Chirality :  0.041   0.137   1112
  Planarity :  0.004   0.039   1183
  Dihedral  :  5.351  74.782    952
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.72 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.28), residues: 868
  helix:  2.26 (0.26), residues: 387
  sheet:  0.02 (0.35), residues: 188
  loop : -0.57 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.010   0.001   TYR R 338 
 ARG   0.006   0.000   ARG R  73 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ASN cc_start: 0.6222 (m-40) cc_final: 0.5646 (m-40)
REVERT: A  274 LYS cc_start: 0.6878 (tttt) cc_final: 0.6546 (ttmt)
REVERT: A  314 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6003 (mp0)
REVERT: A  343 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7690 (ttpt)
REVERT: A  371 ASN cc_start: 0.7534 (m-40) cc_final: 0.7215 (m-40)
REVERT: B  217 MET cc_start: 0.7243 (ptt) cc_final: 0.5981 (pmt)
REVERT: B  226 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6262 (mp0)
REVERT: R   45 ILE cc_start: 0.5855 (pt) cc_final: 0.5581 (mt)
REVERT: R  118 THR cc_start: 0.7042 (m) cc_final: 0.6807 (m)
REVERT: R  160 LYS cc_start: 0.5971 (mmtp) cc_final: 0.5693 (tmtt)
REVERT: R  235 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5924 (mt-10)
REVERT: R  338 TYR cc_start: 0.7196 (m-80) cc_final: 0.6858 (m-80)
REVERT: R  346 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5784 (tpm170)
REVERT: R  369 ILE cc_start: 0.6710 (tt) cc_final: 0.6355 (pt)
  outliers start: 20
  outliers final: 9
  residues processed: 118
  average time/residue: 1.2205
  time to fit residues: 151.5676
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain P residue    3 MET
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0020
   chunk 75 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.202537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.157906 restraints weight = 7146.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.11
r_work: 0.3898 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6945  Z= 0.167
  Angle     :  0.549   7.927   9440  Z= 0.289
  Chirality :  0.042   0.135   1112
  Planarity :  0.004   0.039   1183
  Dihedral  :  5.352  73.730    952
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.85 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.28), residues: 868
  helix:  2.32 (0.26), residues: 386
  sheet:  0.09 (0.35), residues: 186
  loop : -0.59 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.016   0.001   HIS A 220 
 PHE   0.018   0.001   PHE R  93 
 TYR   0.010   0.001   TYR R 338 
 ARG   0.008   0.001   ARG B 251 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6703 (mt)
REVERT: A  271 ASN cc_start: 0.6182 (m-40) cc_final: 0.5618 (m-40)
REVERT: A  274 LYS cc_start: 0.6936 (tttt) cc_final: 0.6608 (ttmt)
REVERT: A  314 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5671 (mp0)
REVERT: A  343 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7708 (ttpt)
REVERT: A  371 ASN cc_start: 0.7567 (m-40) cc_final: 0.7245 (m-40)
REVERT: B   19 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7698 (mtp-110)
REVERT: B  219 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7580 (mmt90)
REVERT: R   45 ILE cc_start: 0.5845 (pt) cc_final: 0.5597 (mt)
REVERT: R  160 LYS cc_start: 0.6078 (mmtp) cc_final: 0.5807 (tmtt)
REVERT: R  205 MET cc_start: 0.5154 (ptp) cc_final: 0.4449 (ppp)
REVERT: R  235 GLU cc_start: 0.6614 (mm-30) cc_final: 0.5967 (mt-10)
REVERT: R  338 TYR cc_start: 0.7143 (m-80) cc_final: 0.6808 (m-80)
REVERT: R  346 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5690 (tpm170)
  outliers start: 17
  outliers final: 10
  residues processed: 114
  average time/residue: 1.2261
  time to fit residues: 147.1338
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain P residue    3 MET
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  359 SER
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 21 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0970
   chunk 55 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.203475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.159247 restraints weight = 7173.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 2.09
r_work: 0.3913 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3785 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7120
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6945  Z= 0.150
  Angle     :  0.539   8.503   9440  Z= 0.284
  Chirality :  0.042   0.194   1112
  Planarity :  0.004   0.039   1183
  Dihedral  :  5.236  70.996    952
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.27 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.29), residues: 868
  helix:  2.45 (0.26), residues: 385
  sheet:  0.06 (0.35), residues: 186
  loop : -0.54 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 338 
 ARG   0.008   0.001   ARG B 251 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6678 (mt)
REVERT: A  271 ASN cc_start: 0.6172 (m-40) cc_final: 0.5548 (m-40)
REVERT: A  314 GLU cc_start: 0.6307 (mt-10) cc_final: 0.5618 (mp0)
REVERT: A  343 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7716 (ttpt)
REVERT: A  371 ASN cc_start: 0.7531 (m-40) cc_final: 0.7212 (m-40)
REVERT: B   19 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7686 (mtp-110)
REVERT: B  219 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7642 (mmt90)
REVERT: R   45 ILE cc_start: 0.5846 (pt) cc_final: 0.5623 (mt)
REVERT: R   73 ARG cc_start: 0.7527 (tpp80) cc_final: 0.7325 (tpp80)
REVERT: R  160 LYS cc_start: 0.6177 (mmtp) cc_final: 0.5830 (tmtt)
REVERT: R  235 GLU cc_start: 0.6493 (mm-30) cc_final: 0.5923 (mt-10)
REVERT: R  338 TYR cc_start: 0.7136 (m-80) cc_final: 0.6797 (m-80)
REVERT: R  346 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5626 (tpm170)
  outliers start: 15
  outliers final: 8
  residues processed: 114
  average time/residue: 1.2360
  time to fit residues: 148.2538
Evaluate side-chains
  110 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  172 ILE
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  374 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0170
   chunk 34 optimal weight:    0.8980
   chunk 8 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.204487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.160641 restraints weight = 7284.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 2.10
r_work: 0.3928 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3801 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6945  Z= 0.146
  Angle     :  0.540  11.031   9440  Z= 0.282
  Chirality :  0.041   0.143   1112
  Planarity :  0.004   0.039   1183
  Dihedral  :  5.111  67.168    952
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.97 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.29), residues: 868
  helix:  2.55 (0.26), residues: 385
  sheet:  0.04 (0.35), residues: 188
  loop : -0.51 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.018   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 338 
 ARG   0.007   0.001   ARG R  73 

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ASN cc_start: 0.6129 (m-40) cc_final: 0.5569 (m-40)
REVERT: A  274 LYS cc_start: 0.6924 (tttt) cc_final: 0.6594 (ttmp)
REVERT: A  314 GLU cc_start: 0.6237 (mt-10) cc_final: 0.5596 (mp0)
REVERT: A  343 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7798 (ttpt)
REVERT: A  371 ASN cc_start: 0.7402 (m-40) cc_final: 0.7086 (m-40)
REVERT: B   19 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7697 (mtp-110)
REVERT: R   45 ILE cc_start: 0.5819 (pt) cc_final: 0.5607 (mt)
REVERT: R  160 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5850 (tmtt)
REVERT: R  205 MET cc_start: 0.5038 (ptp) cc_final: 0.4365 (ppp)
REVERT: R  223 VAL cc_start: 0.6806 (t) cc_final: 0.6586 (t)
REVERT: R  238 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5994 (tt0)
REVERT: R  346 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5554 (tpm170)
  outliers start: 13
  outliers final: 6
  residues processed: 114
  average time/residue: 1.1622
  time to fit residues: 139.7568
Evaluate side-chains
  107 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain R residue  238 GLN
Chi-restraints excluded: chain R residue  338 TYR
Chi-restraints excluded: chain R residue  346 ARG
Chi-restraints excluded: chain R residue  362 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 83 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0570
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
R 374 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.203497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.159565 restraints weight = 7241.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 2.11
r_work: 0.3915 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6945  Z= 0.158
  Angle     :  0.552  10.334   9440  Z= 0.289
  Chirality :  0.041   0.138   1112
  Planarity :  0.004   0.042   1183
  Dihedral  :  4.463  26.955    951
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 23.10 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.29), residues: 868
  helix:  2.56 (0.26), residues: 384
  sheet:  0.07 (0.35), residues: 188
  loop : -0.50 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.024   0.002   PHE R  52 
 TYR   0.010   0.001   TYR R 176 
 ARG   0.007   0.001   ARG B 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7213.23 seconds
wall clock time: 123 minutes 5.66 seconds (7385.66 seconds total)