Starting phenix.real_space_refine
on Thu Jul 31 23:04:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s0g_24790/07_2025/7s0g_24790_trim.cif"
  }
  resolution = 3.86
  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=  -0.000 sd=   0.968
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: 5
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     C    4451      2.51       5
     N    1198      2.21       5
     O    1292      1.98       5
     H    6854      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13846
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 4248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 4248
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 10, 'TRANS': 263}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 5098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5098
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 3526
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 959
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 4, 'TRANS': 55}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'5FW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.35, per 1000 atoms: 0.53
  Number of scatterers: 13846
  At special positions: 0
  Unit cell: (84.8065, 98.762, 130.967, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      51     16.00
     O    1292      8.00
     N    1198      7.00
     C    4451      6.00
     H    6854      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 192 " - pdb=" SG  CYS R 198 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.80
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      47.5% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'R' and resid 40 through 69
      removed outlier: 3.915A  pdb=" N   LEU R  46 " --> pdb=" O   ALA R  42 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU R  47 " --> pdb=" O   GLY R  43 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR R  69 " --> pdb=" O   ALA R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 105
      removed outlier: 3.591A  pdb=" N   LEU R  78 " --> pdb=" O   THR R  74 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   PHE R  79 " --> pdb=" O   LEU R  75 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   VAL R  95 " --> pdb=" O   GLY R  91 " (cutoff:3.500A)
      Proline residue:  R  96  - end of helix
    Processing helix  chain 'R' and resid 110 through 145
    Processing helix  chain 'R' and resid 145 through 153
    Processing helix  chain 'R' and resid 154 through 179
      removed outlier: 4.186A  pdb=" N   LEU R 175 " --> pdb=" O   LEU R 171 " (cutoff:3.500A)
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 186 through 195
    Processing helix  chain 'R' and resid 204 through 216
      removed outlier: 3.745A  pdb=" N   ALA R 208 " --> pdb=" O   ASN R 204 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 241
    Processing helix  chain 'R' and resid 286 through 316
      removed outlier: 3.672A  pdb=" N   ILE R 295 " --> pdb=" O   THR R 291 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE R 299 " --> pdb=" O   ILE R 295 " (cutoff:3.500A)
      Proline residue:  R 305  - end of helix
      removed outlier: 3.584A  pdb=" N   VAL R 314 " --> pdb=" O   ASN R 310 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   PHE R 315 " --> pdb=" O   ILE R 311 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN R 316 " --> pdb=" O   VAL R 312 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 320
      removed outlier: 3.665A  pdb=" N   VAL R 320 " --> pdb=" O   ARG R 317 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 317 through 320'
    Processing helix  chain 'R' and resid 321 through 344
      removed outlier: 3.747A  pdb=" N   PHE R 325 " --> pdb=" O   PRO R 321 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN R 335 " --> pdb=" O   LEU R 331 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   SER R 336 " --> pdb=" O   GLY R 332 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA R 337 " --> pdb=" O   TYR R 333 " (cutoff:3.500A)
      Proline residue:  R 340  - end of helix
    Processing helix  chain 'R' and resid 346 through 356
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.612A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.562A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.598A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.677A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.552A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.098A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.101A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.659A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150
      removed outlier: 7.013A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 192
      removed outlier: 6.663A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.611A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.746A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   VAL B 296 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191
      removed outlier: 7.827A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1095 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: 4.76

  Time building geometry restraints manager: 4.61 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6828
        1.03 -     1.23: 36
        1.23 -     1.43: 2999
        1.43 -     1.62: 4051
        1.62 -     1.82: 72
  Bond restraints: 13986
  Sorted by residual:
  bond pdb=" CAM 5FW R 401 "
       pdb=" OAB 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.353  1.438 -0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" CAO 5FW R 401 "
       pdb=" OAC 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.417 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CAG 5FW R 401 "
       pdb=" NAD 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 2.00e-02 2.50e+03 3.26e+00
  bond pdb=" CAE 5FW R 401 "
       pdb=" CAH 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.515  1.546 -0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" CAG 5FW R 401 "
       pdb=" CAJ 5FW R 401 "
    ideal  model  delta    sigma   weight residual
    1.530  1.501  0.029 2.00e-02 2.50e+03 2.16e+00
  ... (remaining 13981 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.99: 25180
       21.99 -    43.98: 0
       43.98 -    65.97: 0
       65.97 -    87.96: 0
       87.96 -   109.94: 1
  Bond angle restraints: 25181
  Sorted by residual:
  angle pdb=" HB2 GLU A 352 "
        pdb=" CB  GLU A 352 "
        pdb=" HB3 GLU A 352 "
      ideal   model   delta    sigma   weight residual
     110.00    0.06  109.94 3.00e+00 1.11e-01 1.34e+03
  angle pdb=" C   VAL R  95 "
        pdb=" CA  VAL R  95 "
        pdb=" CB  VAL R  95 "
      ideal   model   delta    sigma   weight residual
     114.00  110.72    3.28 1.31e+00 5.83e-01 6.28e+00
  angle pdb=" N   VAL A 201 "
        pdb=" CA  VAL A 201 "
        pdb=" C   VAL A 201 "
      ideal   model   delta    sigma   weight residual
     111.88  109.50    2.38 1.06e+00 8.90e-01 5.03e+00
  angle pdb=" C   VAL R  94 "
        pdb=" N   VAL R  95 "
        pdb=" CA  VAL R  95 "
      ideal   model   delta    sigma   weight residual
     120.33  122.02   -1.69 8.00e-01 1.56e+00 4.44e+00
  angle pdb=" CAJ 5FW R 401 "
        pdb=" CAG 5FW R 401 "
        pdb=" NAD 5FW R 401 "
      ideal   model   delta    sigma   weight residual
     114.52  109.00    5.52 3.00e+00 1.11e-01 3.39e+00
  ... (remaining 25176 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.60: 5984
       15.60 -    31.20: 449
       31.20 -    46.81: 97
       46.81 -    62.41: 50
       62.41 -    78.01: 7
  Dihedral angle restraints: 6587
    sinusoidal: 3491
      harmonic: 3096
  Sorted by residual:
  dihedral pdb=" CA  ASP B 153 "
           pdb=" CB  ASP B 153 "
           pdb=" CG  ASP B 153 "
           pdb=" OD1 ASP B 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.44   52.44     1      2.00e+01 2.50e-03 9.37e+00
  dihedral pdb=" CA  ASP B 312 "
           pdb=" CB  ASP B 312 "
           pdb=" CG  ASP B 312 "
           pdb=" OD1 ASP B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.17   52.17     1      2.00e+01 2.50e-03 9.28e+00
  dihedral pdb=" CA  ASN R 310 "
           pdb=" CB  ASN R 310 "
           pdb=" CG  ASN R 310 "
           pdb=" OD1 ASN R 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00  178.63  -58.63     2      2.00e+01 2.50e-03 8.75e+00
  ... (remaining 6584 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 984
       0.057 -    0.114: 111
       0.114 -    0.171: 11
       0.171 -    0.229: 0
       0.229 -    0.286: 1
  Chirality restraints: 1107
  Sorted by residual:
  chirality pdb=" CAE 5FW R 401 "
            pdb=" CAF 5FW R 401 "
            pdb=" CAH 5FW R 401 "
            pdb=" OAA 5FW R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.58    0.29 2.00e-01 2.50e+01 2.04e+00
  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   -0.13 2.00e-01 2.50e+01 4.28e-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 4.25e-01
  ... (remaining 1104 not shown)

  Planarity restraints: 2090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.019 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO G  49 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 218 "    0.018 5.00e-02 4.00e+02   2.77e-02 1.23e+00
        pdb=" N   PRO R 219 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO R 219 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO R 219 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 320 "   -0.016 5.00e-02 4.00e+02   2.39e-02 9.13e-01
        pdb=" N   PRO R 321 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO R 321 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO R 321 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 2087 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 1067
        2.23 -     2.82: 30218
        2.82 -     3.41: 35336
        3.41 -     4.01: 47215
        4.01 -     4.60: 73202
  Nonbonded interactions: 187038
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     1.635 2.450
  nonbonded pdb=" OE1 GLU A 289 "
            pdb=" H   GLU A 289 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" HG  SER B 207 "
     model   vdw
     1.668 2.450
  nonbonded pdb=" OD1 ASP R 184 "
            pdb=" H   ASP R 186 "
     model   vdw
     1.681 2.450
  nonbonded pdb="HH11 ARG B 251 "
            pdb=" OE2 GLU B 260 "
     model   vdw
     1.686 2.450
  ... (remaining 187033 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 group one per residue
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:             1.560
  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:             0.250
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.090
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   7134  Z= 0.143
  Angle     :  0.441   5.523   9673  Z= 0.261
  Chirality :  0.037   0.286   1107
  Planarity :  0.002   0.029   1224
  Dihedral  : 12.412  78.012   2543
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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: -1.90 (0.27), residues: 881
  helix:  0.26 (0.24), residues: 403
  sheet: -2.74 (0.35), residues: 158
  loop : -2.36 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 117 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.009   0.001   PHE R 174 
 TYR   0.008   0.001   TYR G  40 
 ARG   0.001   0.000   ARG R 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09844 (  378)
  hydrogen bonds       : angle       4.43579 ( 1095)
  SS BOND              : bond        0.00084 (    2)
  SS BOND              : angle       0.60446 (    4)
  covalent geometry    : bond        0.00274 ( 7132)
  covalent geometry    : angle       0.44098 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  322 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  116 LEU cc_start: 0.8061 (tt) cc_final: 0.7857 (tt)
REVERT: R  236 GLU cc_start: 0.8452 (tt0) cc_final: 0.8201 (tt0)
REVERT: R  240 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8394 (mttt)
REVERT: R  285 GLU cc_start: 0.7637 (pm20) cc_final: 0.7348 (mt-10)
REVERT: R  323 TRP cc_start: 0.7904 (p-90) cc_final: 0.7507 (p-90)
REVERT: B   68 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7888 (ttt180)
REVERT: B   75 GLN cc_start: 0.7283 (mt0) cc_final: 0.6931 (mt0)
REVERT: B   97 SER cc_start: 0.9234 (t) cc_final: 0.8826 (p)
REVERT: B  134 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6701 (mtp-110)
REVERT: B  176 GLN cc_start: 0.8763 (mt0) cc_final: 0.8447 (mt0)
REVERT: B  228 ASP cc_start: 0.8307 (m-30) cc_final: 0.8064 (m-30)
REVERT: B  237 ASN cc_start: 0.9048 (t0) cc_final: 0.8781 (t0)
REVERT: B  247 ASP cc_start: 0.7841 (t0) cc_final: 0.7453 (t0)
REVERT: B  304 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7491 (ttp80)
REVERT: B  321 THR cc_start: 0.9297 (p) cc_final: 0.9062 (p)
REVERT: A   16 SER cc_start: 0.8901 (p) cc_final: 0.8666 (p)
REVERT: A   22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (m110)
REVERT: A  214 CYS cc_start: 0.8533 (m) cc_final: 0.8031 (t)
REVERT: A  312 LYS cc_start: 0.8307 (mttt) cc_final: 0.7964 (mmmt)
REVERT: A  330 LYS cc_start: 0.8574 (mttt) cc_final: 0.8365 (mmtp)
REVERT: G   27 ARG cc_start: 0.7354 (mtt-85) cc_final: 0.6339 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.4873
  time to fit residues: 203.4173
Evaluate side-chains
  266 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
R 150 GLN
R 237 GLN
R 310 ASN
B  75 GLN
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.147727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.115954 restraints weight = 24297.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.122116 restraints weight = 11566.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.126295 restraints weight = 7177.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7134  Z= 0.169
  Angle     :  0.500   5.370   9673  Z= 0.271
  Chirality :  0.038   0.148   1107
  Planarity :  0.003   0.035   1224
  Dihedral  :  3.441  13.723    970
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.09 %
    Favored  : 83.56 %
  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: -0.95 (0.28), residues: 881
  helix:  1.43 (0.26), residues: 407
  sheet: -2.90 (0.34), residues: 155
  loop : -2.16 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 117 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.007   0.001   TYR B 289 
 ARG   0.005   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03604 (  378)
  hydrogen bonds       : angle       4.07204 ( 1095)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.79051 (    4)
  covalent geometry    : bond        0.00363 ( 7132)
  covalent geometry    : angle       0.49905 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  293 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 283
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8166 (mt-10)
REVERT: R  150 GLN cc_start: 0.8343 (tp40) cc_final: 0.8114 (tp-100)
REVERT: R  236 GLU cc_start: 0.8391 (tt0) cc_final: 0.8109 (tt0)
REVERT: R  237 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7417 (tp40)
REVERT: R  285 GLU cc_start: 0.7654 (pm20) cc_final: 0.7448 (mt-10)
REVERT: R  323 TRP cc_start: 0.8188 (p-90) cc_final: 0.7449 (p-90)
REVERT: B   97 SER cc_start: 0.9214 (t) cc_final: 0.8815 (p)
REVERT: B  134 ARG cc_start: 0.6973 (mmm-85) cc_final: 0.6689 (mtp-110)
REVERT: B  176 GLN cc_start: 0.8728 (mt0) cc_final: 0.8396 (mt0)
REVERT: B  228 ASP cc_start: 0.8282 (m-30) cc_final: 0.8021 (m-30)
REVERT: B  247 ASP cc_start: 0.7948 (t0) cc_final: 0.7525 (t0)
REVERT: B  304 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7527 (ttp80)
REVERT: B  325 MET cc_start: 0.8021 (mmt) cc_final: 0.7525 (mmt)
REVERT: A   16 SER cc_start: 0.8979 (p) cc_final: 0.8645 (p)
REVERT: A   22 ASN cc_start: 0.8512 (m-40) cc_final: 0.8247 (m110)
REVERT: A   25 GLU cc_start: 0.7673 (tp30) cc_final: 0.7453 (tp30)
REVERT: A  214 CYS cc_start: 0.8575 (m) cc_final: 0.7970 (t)
REVERT: A  286 CYS cc_start: 0.8334 (p) cc_final: 0.7607 (t)
REVERT: A  330 LYS cc_start: 0.8520 (mttt) cc_final: 0.8216 (mmtp)
REVERT: A  333 GLN cc_start: 0.8751 (tt0) cc_final: 0.8516 (tp40)
REVERT: G   27 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.6914 (mtt-85)
  outliers start: 10
  outliers final: 10
  residues processed: 286
  average time/residue: 0.4360
  time to fit residues: 163.3718
Evaluate side-chains
  285 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 275
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  177 ILE
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 81 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** A 306 GLN ** 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 = 0.3563 r_free = 0.3563 target = 0.144712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.113062 restraints weight = 24834.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.119138 restraints weight = 11773.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.123110 restraints weight = 7297.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7134  Z= 0.206
  Angle     :  0.512   7.437   9673  Z= 0.280
  Chirality :  0.038   0.123   1107
  Planarity :  0.004   0.058   1224
  Dihedral  :  3.703  16.537    970
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.90 %
    Favored  : 81.13 %
  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: -0.67 (0.28), residues: 881
  helix:  1.76 (0.26), residues: 407
  sheet: -2.87 (0.34), residues: 160
  loop : -2.07 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 117 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.013   0.002   TYR B  85 
 ARG   0.008   0.001   ARG R 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  378)
  hydrogen bonds       : angle       4.16319 ( 1095)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       0.88179 (    4)
  covalent geometry    : bond        0.00434 ( 7132)
  covalent geometry    : angle       0.51223 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  307 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 285
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  116 LEU cc_start: 0.8124 (tt) cc_final: 0.7921 (tt)
REVERT: R  236 GLU cc_start: 0.8366 (tt0) cc_final: 0.8133 (tt0)
REVERT: R  285 GLU cc_start: 0.7724 (pm20) cc_final: 0.7448 (mt-10)
REVERT: R  323 TRP cc_start: 0.8310 (p-90) cc_final: 0.7494 (p-90)
REVERT: B   97 SER cc_start: 0.9238 (t) cc_final: 0.8902 (p)
REVERT: B  134 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6751 (mtp-110)
REVERT: B  228 ASP cc_start: 0.8281 (m-30) cc_final: 0.7948 (m-30)
REVERT: B  247 ASP cc_start: 0.8022 (t0) cc_final: 0.7564 (t0)
REVERT: B  304 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7521 (ttp80)
REVERT: B  325 MET cc_start: 0.8015 (mmt) cc_final: 0.7586 (mmt)
REVERT: A   16 SER cc_start: 0.8983 (p) cc_final: 0.8723 (p)
REVERT: A   22 ASN cc_start: 0.8615 (m-40) cc_final: 0.8315 (m110)
REVERT: A  214 CYS cc_start: 0.8563 (m) cc_final: 0.7688 (t)
REVERT: A  248 LYS cc_start: 0.8876 (mttp) cc_final: 0.8476 (mtpt)
REVERT: A  286 CYS cc_start: 0.8268 (p) cc_final: 0.7646 (t)
REVERT: A  289 GLU cc_start: 0.7440 (pm20) cc_final: 0.6942 (pm20)
REVERT: A  330 LYS cc_start: 0.8541 (mttt) cc_final: 0.8236 (mmtp)
REVERT: A  333 GLN cc_start: 0.8825 (tt0) cc_final: 0.8538 (tp40)
REVERT: G   27 ARG cc_start: 0.7461 (mtt-85) cc_final: 0.6998 (mtt-85)
REVERT: G   46 LYS cc_start: 0.8730 (mttp) cc_final: 0.8389 (mtpp)
  outliers start: 22
  outliers final: 20
  residues processed: 290
  average time/residue: 0.4082
  time to fit residues: 155.6115
Evaluate side-chains
  290 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 270
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain R residue  222 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.146344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.115073 restraints weight = 24363.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.121214 restraints weight = 11503.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.125236 restraints weight = 7056.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7134  Z= 0.136
  Angle     :  0.485   7.009   9673  Z= 0.262
  Chirality :  0.038   0.131   1107
  Planarity :  0.003   0.040   1224
  Dihedral  :  3.608  19.090    970
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.73 %
    Favored  : 78.84 %
  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: -0.34 (0.29), residues: 881
  helix:  2.06 (0.25), residues: 407
  sheet: -2.71 (0.36), residues: 156
  loop : -1.96 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  82 
 HIS   0.010   0.001   HIS R 180 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.008   0.001   TYR G  40 
 ARG   0.004   0.000   ARG R 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  378)
  hydrogen bonds       : angle       3.98335 ( 1095)
  SS BOND              : bond        0.00429 (    2)
  SS BOND              : angle       1.37777 (    4)
  covalent geometry    : bond        0.00293 ( 7132)
  covalent geometry    : angle       0.48458 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  296 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 278
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: R  150 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7982 (tp-100)
REVERT: R  236 GLU cc_start: 0.8365 (tt0) cc_final: 0.8097 (tt0)
REVERT: R  285 GLU cc_start: 0.7773 (pm20) cc_final: 0.7499 (mt-10)
REVERT: R  323 TRP cc_start: 0.8159 (p-90) cc_final: 0.7362 (p-90)
REVERT: B   57 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7967 (ptmt)
REVERT: B   97 SER cc_start: 0.9271 (t) cc_final: 0.8868 (p)
REVERT: B  134 ARG cc_start: 0.6998 (mmm-85) cc_final: 0.6711 (mtp-110)
REVERT: B  228 ASP cc_start: 0.8240 (m-30) cc_final: 0.7945 (m-30)
REVERT: B  247 ASP cc_start: 0.7996 (t0) cc_final: 0.7536 (t0)
REVERT: B  304 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7566 (ttp80)
REVERT: B  325 MET cc_start: 0.8035 (mmt) cc_final: 0.7556 (mmt)
REVERT: A   16 SER cc_start: 0.8920 (p) cc_final: 0.8713 (p)
REVERT: A   22 ASN cc_start: 0.8510 (m-40) cc_final: 0.8211 (m110)
REVERT: A   25 GLU cc_start: 0.7640 (tp30) cc_final: 0.7402 (tp30)
REVERT: A  283 LEU cc_start: 0.8270 (tp) cc_final: 0.7996 (tt)
REVERT: A  286 CYS cc_start: 0.8130 (p) cc_final: 0.7570 (t)
REVERT: A  330 LYS cc_start: 0.8490 (mttt) cc_final: 0.8200 (mmtp)
REVERT: G   27 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6979 (mtt-85)
REVERT: G   46 LYS cc_start: 0.8709 (mttp) cc_final: 0.8367 (mtpp)
  outliers start: 18
  outliers final: 16
  residues processed: 282
  average time/residue: 0.4158
  time to fit residues: 154.4604
Evaluate side-chains
  286 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 270
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0060
   chunk 83 optimal weight:    6.9990
   overall best weight:    0.7198

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.145851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.114782 restraints weight = 24683.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.120913 restraints weight = 11486.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.124952 restraints weight = 7065.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7134  Z= 0.142
  Angle     :  0.492   6.787   9673  Z= 0.265
  Chirality :  0.038   0.163   1107
  Planarity :  0.004   0.049   1224
  Dihedral  :  3.622  19.049    970
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.14 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.16 (0.29), residues: 881
  helix:  2.29 (0.25), residues: 401
  sheet: -2.74 (0.37), residues: 149
  loop : -1.88 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 213 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.008   0.001   TYR G  40 
 ARG   0.005   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  378)
  hydrogen bonds       : angle       3.95045 ( 1095)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       1.76244 (    4)
  covalent geometry    : bond        0.00307 ( 7132)
  covalent geometry    : angle       0.49047 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  296 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 278
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: R  150 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7939 (tp-100)
REVERT: R  188 GLN cc_start: 0.7085 (tp40) cc_final: 0.6401 (tm-30)
REVERT: R  236 GLU cc_start: 0.8336 (tt0) cc_final: 0.8098 (tt0)
REVERT: R  285 GLU cc_start: 0.7833 (pm20) cc_final: 0.7527 (mt-10)
REVERT: R  323 TRP cc_start: 0.8147 (p-90) cc_final: 0.7365 (p-90)
REVERT: B   57 LYS cc_start: 0.8316 (ptpt) cc_final: 0.7978 (ptmt)
REVERT: B   97 SER cc_start: 0.9322 (t) cc_final: 0.8919 (p)
REVERT: B  134 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6683 (mtp-110)
REVERT: B  228 ASP cc_start: 0.8215 (m-30) cc_final: 0.7894 (m-30)
REVERT: B  247 ASP cc_start: 0.7904 (t0) cc_final: 0.7412 (t0)
REVERT: B  304 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7494 (ttp80)
REVERT: B  325 MET cc_start: 0.8026 (mmt) cc_final: 0.7540 (mmt)
REVERT: A   22 ASN cc_start: 0.8476 (m-40) cc_final: 0.8191 (m110)
REVERT: A   25 GLU cc_start: 0.7663 (tp30) cc_final: 0.7407 (tp30)
REVERT: A  248 LYS cc_start: 0.8868 (mttp) cc_final: 0.8463 (mtpt)
REVERT: A  261 ASP cc_start: 0.8797 (p0) cc_final: 0.8539 (p0)
REVERT: A  333 GLN cc_start: 0.8743 (tt0) cc_final: 0.8070 (tp-100)
REVERT: G   27 ARG cc_start: 0.7388 (mtt-85) cc_final: 0.6992 (mtt-85)
REVERT: G   46 LYS cc_start: 0.8698 (mttp) cc_final: 0.8364 (mtpp)
  outliers start: 18
  outliers final: 18
  residues processed: 283
  average time/residue: 0.4291
  time to fit residues: 160.0273
Evaluate side-chains
  278 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 260
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  168 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.144866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.114005 restraints weight = 24840.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.120127 restraints weight = 11551.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.124228 restraints weight = 7090.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7134  Z= 0.158
  Angle     :  0.499   8.518   9673  Z= 0.269
  Chirality :  0.038   0.127   1107
  Planarity :  0.003   0.041   1224
  Dihedral  :  3.649  18.675    970
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.73 %
    Favored  : 78.30 %
  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: -0.03 (0.29), residues: 881
  helix:  2.42 (0.25), residues: 401
  sheet: -2.72 (0.37), residues: 153
  loop : -1.81 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.017   0.001   TYR A 351 
 ARG   0.004   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  378)
  hydrogen bonds       : angle       3.97420 ( 1095)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       1.56643 (    4)
  covalent geometry    : bond        0.00336 ( 7132)
  covalent geometry    : angle       0.49831 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  284 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 262
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7900 (mt-10)
REVERT: R  150 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7965 (tp-100)
REVERT: R  188 GLN cc_start: 0.7087 (tp40) cc_final: 0.6419 (tm-30)
REVERT: R  236 GLU cc_start: 0.8312 (tt0) cc_final: 0.8084 (tt0)
REVERT: R  285 GLU cc_start: 0.7868 (pm20) cc_final: 0.7528 (mt-10)
REVERT: R  323 TRP cc_start: 0.8137 (p-90) cc_final: 0.7347 (p-90)
REVERT: B   57 LYS cc_start: 0.8331 (ptpt) cc_final: 0.8032 (ptmt)
REVERT: B   97 SER cc_start: 0.9315 (t) cc_final: 0.8910 (p)
REVERT: B  134 ARG cc_start: 0.6814 (mmm-85) cc_final: 0.6545 (mtp-110)
REVERT: B  228 ASP cc_start: 0.8187 (m-30) cc_final: 0.7860 (m-30)
REVERT: B  247 ASP cc_start: 0.7923 (t0) cc_final: 0.7435 (t0)
REVERT: B  304 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7494 (ttp80)
REVERT: B  325 MET cc_start: 0.8017 (mmt) cc_final: 0.7555 (mmt)
REVERT: A   22 ASN cc_start: 0.8477 (m-40) cc_final: 0.8199 (m110)
REVERT: A  248 LYS cc_start: 0.8888 (mttp) cc_final: 0.8479 (mtpt)
REVERT: A  261 ASP cc_start: 0.8827 (p0) cc_final: 0.8562 (p0)
REVERT: A  286 CYS cc_start: 0.8257 (p) cc_final: 0.7666 (t)
REVERT: A  333 GLN cc_start: 0.8766 (tt0) cc_final: 0.8085 (tp-100)
REVERT: G   27 ARG cc_start: 0.7390 (mtt-85) cc_final: 0.6995 (mtt-85)
  outliers start: 22
  outliers final: 19
  residues processed: 268
  average time/residue: 0.4105
  time to fit residues: 146.5361
Evaluate side-chains
  275 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 256
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.144572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.113674 restraints weight = 24831.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.119798 restraints weight = 11558.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.123795 restraints weight = 7064.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7134  Z= 0.167
  Angle     :  0.505   8.570   9673  Z= 0.274
  Chirality :  0.038   0.136   1107
  Planarity :  0.003   0.042   1224
  Dihedral  :  3.702  18.709    970
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.87 %
    Favored  : 78.17 %
  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:  0.02 (0.29), residues: 881
  helix:  2.42 (0.25), residues: 402
  sheet: -2.66 (0.38), residues: 153
  loop : -1.75 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.005   0.001   HIS R 180 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.003   0.000   ARG R 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  378)
  hydrogen bonds       : angle       4.01808 ( 1095)
  SS BOND              : bond        0.00016 (    2)
  SS BOND              : angle       1.56393 (    4)
  covalent geometry    : bond        0.00355 ( 7132)
  covalent geometry    : angle       0.50389 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  275 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 253
  time to evaluate  : 1.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: R  150 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7985 (tp-100)
REVERT: R  188 GLN cc_start: 0.7115 (tp40) cc_final: 0.6451 (tm-30)
REVERT: R  236 GLU cc_start: 0.8329 (tt0) cc_final: 0.8095 (tt0)
REVERT: B   57 LYS cc_start: 0.8369 (ptpt) cc_final: 0.8042 (ptmt)
REVERT: B   97 SER cc_start: 0.9336 (t) cc_final: 0.8920 (p)
REVERT: B  134 ARG cc_start: 0.6831 (mmm-85) cc_final: 0.6549 (mtp-110)
REVERT: B  176 GLN cc_start: 0.8736 (mt0) cc_final: 0.8417 (mt0)
REVERT: B  228 ASP cc_start: 0.8155 (m-30) cc_final: 0.7824 (m-30)
REVERT: B  247 ASP cc_start: 0.7935 (t0) cc_final: 0.7451 (t0)
REVERT: B  304 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7490 (ttp80)
REVERT: A   22 ASN cc_start: 0.8487 (m-40) cc_final: 0.8205 (m110)
REVERT: A  248 LYS cc_start: 0.8903 (mttp) cc_final: 0.8489 (mtpt)
REVERT: A  286 CYS cc_start: 0.8240 (p) cc_final: 0.7677 (t)
REVERT: G   27 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.6996 (mtt-85)
  outliers start: 22
  outliers final: 22
  residues processed: 260
  average time/residue: 0.4639
  time to fit residues: 160.6255
Evaluate side-chains
  276 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 254
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  222 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 43 optimal weight:    0.2980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.144010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.113283 restraints weight = 24766.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.119399 restraints weight = 11545.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.123442 restraints weight = 7076.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7134  Z= 0.169
  Angle     :  0.493   4.902   9673  Z= 0.271
  Chirality :  0.038   0.131   1107
  Planarity :  0.004   0.049   1224
  Dihedral  :  3.746  19.079    970
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.00 %
    Favored  : 78.17 %
  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:  0.04 (0.29), residues: 881
  helix:  2.42 (0.25), residues: 402
  sheet: -2.61 (0.38), residues: 153
  loop : -1.74 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.009   0.001   TYR B 105 
 ARG   0.007   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  378)
  hydrogen bonds       : angle       4.01856 ( 1095)
  SS BOND              : bond        0.00049 (    2)
  SS BOND              : angle       1.86756 (    4)
  covalent geometry    : bond        0.00359 ( 7132)
  covalent geometry    : angle       0.49161 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  274 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 253
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7893 (mt-10)
REVERT: R  150 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8011 (tp-100)
REVERT: R  188 GLN cc_start: 0.7147 (tp40) cc_final: 0.6491 (tm-30)
REVERT: R  236 GLU cc_start: 0.8360 (tt0) cc_final: 0.8113 (tt0)
REVERT: B   57 LYS cc_start: 0.8355 (ptpt) cc_final: 0.8040 (ptmt)
REVERT: B   97 SER cc_start: 0.9326 (t) cc_final: 0.8905 (p)
REVERT: B  134 ARG cc_start: 0.6876 (mmm-85) cc_final: 0.6561 (mtp-110)
REVERT: B  176 GLN cc_start: 0.8784 (mt0) cc_final: 0.8473 (mt0)
REVERT: B  228 ASP cc_start: 0.8153 (m-30) cc_final: 0.7833 (m-30)
REVERT: B  247 ASP cc_start: 0.7968 (t0) cc_final: 0.7514 (t0)
REVERT: B  304 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7481 (ttp80)
REVERT: A   22 ASN cc_start: 0.8513 (m-40) cc_final: 0.8252 (m110)
REVERT: A  216 GLU cc_start: 0.8326 (tp30) cc_final: 0.7537 (tp30)
REVERT: A  248 LYS cc_start: 0.8877 (mttp) cc_final: 0.8470 (mtpt)
REVERT: A  286 CYS cc_start: 0.8215 (p) cc_final: 0.7989 (t)
REVERT: A  298 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7410 (tt0)
REVERT: G   27 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7050 (mtt-85)
  outliers start: 21
  outliers final: 21
  residues processed: 259
  average time/residue: 0.4649
  time to fit residues: 161.7227
Evaluate side-chains
  270 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 249
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  222 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0870
   chunk 18 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3569 r_free = 0.3569 target = 0.145315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.114750 restraints weight = 24476.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.120918 restraints weight = 11387.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.125003 restraints weight = 6960.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7134  Z= 0.124
  Angle     :  0.474   5.062   9673  Z= 0.259
  Chirality :  0.038   0.177   1107
  Planarity :  0.003   0.041   1224
  Dihedral  :  3.648  20.285    970
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.68 %
    Favored  : 77.90 %
  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:  0.22 (0.29), residues: 881
  helix:  2.57 (0.25), residues: 402
  sheet: -2.54 (0.38), residues: 153
  loop : -1.65 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 169 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.008   0.001   TYR G  40 
 ARG   0.006   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03220 (  378)
  hydrogen bonds       : angle       3.89554 ( 1095)
  SS BOND              : bond        0.00176 (    2)
  SS BOND              : angle       2.15001 (    4)
  covalent geometry    : bond        0.00268 ( 7132)
  covalent geometry    : angle       0.47205 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  272 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 254
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7828 (mt-10)
REVERT: R  150 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7973 (tp-100)
REVERT: R  188 GLN cc_start: 0.7094 (tp40) cc_final: 0.6439 (tm-30)
REVERT: R  236 GLU cc_start: 0.8323 (tt0) cc_final: 0.8088 (tt0)
REVERT: B   57 LYS cc_start: 0.8347 (ptpt) cc_final: 0.8042 (ptmt)
REVERT: B   97 SER cc_start: 0.9340 (t) cc_final: 0.8925 (p)
REVERT: B  134 ARG cc_start: 0.6864 (mmm-85) cc_final: 0.6518 (mtp-110)
REVERT: B  163 ASP cc_start: 0.7457 (t0) cc_final: 0.7184 (t0)
REVERT: B  188 MET cc_start: 0.7643 (mmm) cc_final: 0.7363 (mmm)
REVERT: B  228 ASP cc_start: 0.8139 (m-30) cc_final: 0.7568 (m-30)
REVERT: B  247 ASP cc_start: 0.7914 (t0) cc_final: 0.7456 (t0)
REVERT: B  304 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7489 (ttp80)
REVERT: A   22 ASN cc_start: 0.8457 (m-40) cc_final: 0.8199 (m110)
REVERT: A  216 GLU cc_start: 0.8313 (tp30) cc_final: 0.7567 (tp30)
REVERT: A  248 LYS cc_start: 0.8865 (mttp) cc_final: 0.8468 (mtpt)
REVERT: A  286 CYS cc_start: 0.8084 (p) cc_final: 0.7766 (t)
REVERT: G   27 ARG cc_start: 0.7362 (mtt-85) cc_final: 0.7127 (mtt-85)
  outliers start: 18
  outliers final: 18
  residues processed: 260
  average time/residue: 0.5053
  time to fit residues: 177.8548
Evaluate side-chains
  267 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 249
  time to evaluate  : 1.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0970
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0770
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A 306 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.147453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.116998 restraints weight = 24490.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.123216 restraints weight = 11310.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.127132 restraints weight = 6881.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7134  Z= 0.098
  Angle     :  0.459   5.077   9673  Z= 0.248
  Chirality :  0.038   0.132   1107
  Planarity :  0.003   0.045   1224
  Dihedral  :  3.486  20.992    970
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.62 %
    Favored  : 77.63 %
  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:  0.47 (0.30), residues: 881
  helix:  2.81 (0.25), residues: 403
  sheet: -2.40 (0.39), residues: 143
  loop : -1.63 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.008   0.001   TYR A 302 
 ARG   0.006   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02967 (  378)
  hydrogen bonds       : angle       3.74653 ( 1095)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       2.06489 (    4)
  covalent geometry    : bond        0.00216 ( 7132)
  covalent geometry    : angle       0.45708 ( 9669)

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   44 is missing expected H atoms. Skipping.
Residue LEU   46 is missing expected H atoms. Skipping.
Residue LEU   47 is missing expected H atoms. Skipping.
Residue MET   48 is missing expected H atoms. Skipping.
Residue LEU   50 is missing expected H atoms. Skipping.
Residue LEU   53 is missing expected H atoms. Skipping.
Residue VAL   56 is missing expected H atoms. Skipping.
Residue LEU  113 is missing expected H atoms. Skipping.
Residue LEU  190 is missing expected H atoms. Skipping.
Residue LYS  351 is missing expected H atoms. Skipping.
Residue LYS  354 is missing expected H atoms. Skipping.
Residue LYS   10 is missing expected H atoms. Skipping.
Residue LYS   17 is missing expected H atoms. Skipping.
Residue LYS   29 is missing expected H atoms. Skipping.
Evaluate side-chains
  264 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 251
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  130 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7092 (mt-10)
REVERT: R  150 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7941 (tp-100)
REVERT: R  188 GLN cc_start: 0.7120 (tp40) cc_final: 0.6421 (tm-30)
REVERT: R  236 GLU cc_start: 0.8292 (tt0) cc_final: 0.8057 (tt0)
REVERT: R  323 TRP cc_start: 0.8168 (p-90) cc_final: 0.7348 (p-90)
REVERT: B   57 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8047 (ptmt)
REVERT: B   75 GLN cc_start: 0.7337 (mt0) cc_final: 0.6837 (mm-40)
REVERT: B   97 SER cc_start: 0.9269 (t) cc_final: 0.8823 (p)
REVERT: B  134 ARG cc_start: 0.6826 (mmm-85) cc_final: 0.6490 (mtp-110)
REVERT: B  163 ASP cc_start: 0.7378 (t0) cc_final: 0.7101 (t0)
REVERT: B  188 MET cc_start: 0.7560 (mmm) cc_final: 0.7113 (mmm)
REVERT: B  247 ASP cc_start: 0.7843 (t0) cc_final: 0.7366 (t0)
REVERT: B  304 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7470 (ttp80)
REVERT: A   22 ASN cc_start: 0.8424 (m-40) cc_final: 0.8144 (m110)
REVERT: A  214 CYS cc_start: 0.8419 (m) cc_final: 0.7963 (t)
REVERT: A  216 GLU cc_start: 0.8337 (tp30) cc_final: 0.7638 (tp30)
REVERT: A  248 LYS cc_start: 0.8854 (mttp) cc_final: 0.8465 (mtpt)
REVERT: A  286 CYS cc_start: 0.8169 (p) cc_final: 0.7728 (t)
  outliers start: 13
  outliers final: 12
  residues processed: 257
  average time/residue: 0.4431
  time to fit residues: 151.2544
Evaluate side-chains
  259 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 247
  time to evaluate  : 2.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  263 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain G residue   42 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0770
   chunk 37 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 73 optimal weight:    0.2980
   chunk 61 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.146900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.116365 restraints weight = 24673.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.122627 restraints weight = 11420.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.126715 restraints weight = 6897.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7134  Z= 0.113
  Angle     :  0.460   4.885   9673  Z= 0.250
  Chirality :  0.038   0.129   1107
  Planarity :  0.003   0.051   1224
  Dihedral  :  3.464  20.263    970
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 20.49 %
    Favored  : 77.76 %
  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:  0.52 (0.30), residues: 881
  helix:  2.87 (0.25), residues: 403
  sheet: -2.42 (0.39), residues: 145
  loop : -1.60 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  99 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.013   0.001   TYR A 302 
 ARG   0.006   0.000   ARG R 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02971 (  378)
  hydrogen bonds       : angle       3.73578 ( 1095)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       0.28560 (    4)
  covalent geometry    : bond        0.00247 ( 7132)
  covalent geometry    : angle       0.45977 ( 9669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6651.21 seconds
wall clock time: 118 minutes 44.90 seconds (7124.90 seconds total)