Starting phenix.real_space_refine
on Wed Feb 12 18:21:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w8a_37350/02_2025/8w8a_37350.cif"
  }
  resolution = 2.8
  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=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5250      2.51       5
     N    1422      2.21       5
     O    1525      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8260
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1934
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2597
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 11, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Unusual residues: {'T5U': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 4.98, per 1000 atoms: 0.60
  Number of scatterers: 8260
  At special positions: 0
  Unit cell: (79.04, 99.84, 133.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1525      8.00
     N    1422      7.00
     C    5250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.27
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.35
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.35

  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: 2.18
  Conformation dependent library (CDL) restraints added in 933.5 milliseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      44.0% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 37
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.752A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.129A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 3.690A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.575A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.724A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 86
      removed outlier: 3.685A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 3.562A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 232
    Processing helix  chain 'R' and resid 247 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 276 through 280
    Processing helix  chain 'R' and resid 282 through 306
      removed outlier: 3.543A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN R 296 " --> pdb=" O   PHE R 292 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR R 298 " --> pdb=" O   TYR R 294 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 318
      removed outlier: 3.616A  pdb=" N   ARG R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 4.880A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.616A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.753A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.852A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.512A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.719A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.457A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.427A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.588A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 20

    435 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1394
        1.32 -     1.44: 2329
        1.44 -     1.56: 4624
        1.56 -     1.69: 2
        1.69 -     1.81: 92
  Bond restraints: 8441
  Sorted by residual:
  bond pdb=" CA  CYS N  96 "
       pdb=" C   CYS N  96 "
    ideal  model  delta    sigma   weight residual
    1.524  1.447  0.077 1.25e-02 6.40e+03 3.78e+01
  bond pdb=" CA  ASP N 109 "
       pdb=" C   ASP N 109 "
    ideal  model  delta    sigma   weight residual
    1.528  1.477  0.051 1.04e-02 9.25e+03 2.40e+01
  bond pdb=" C13 T5U R 401 "
       pdb=" N03 T5U R 401 "
    ideal  model  delta    sigma   weight residual
    1.275  1.354 -0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" CA  SER R 183 "
       pdb=" C   SER R 183 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.08e-02 8.57e+03 1.54e+01
  bond pdb=" CA  LYS B  57 "
       pdb=" C   LYS B  57 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.048 1.26e-02 6.30e+03 1.46e+01
  ... (remaining 8436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11228
        2.32 -     4.64: 173
        4.64 -     6.97: 20
        6.97 -     9.29: 7
        9.29 -    11.61: 4
  Bond angle restraints: 11432
  Sorted by residual:
  angle pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" C   ASP N 109 "
      ideal   model   delta    sigma   weight residual
     109.71  119.49   -9.78 1.41e+00 5.03e-01 4.81e+01
  angle pdb=" N   ASN A  66 "
        pdb=" CA  ASN A  66 "
        pdb=" C   ASN A  66 "
      ideal   model   delta    sigma   weight residual
     111.30  101.74    9.56 1.43e+00 4.89e-01 4.47e+01
  angle pdb=" N   CYS N  96 "
        pdb=" CA  CYS N  96 "
        pdb=" C   CYS N  96 "
      ideal   model   delta    sigma   weight residual
     110.17  100.08   10.09 1.61e+00 3.86e-01 3.93e+01
  angle pdb=" N   GLY A  68 "
        pdb=" CA  GLY A  68 "
        pdb=" C   GLY A  68 "
      ideal   model   delta    sigma   weight residual
     112.49  119.46   -6.97 1.21e+00 6.83e-01 3.32e+01
  angle pdb=" N   HIS A  64 "
        pdb=" CA  HIS A  64 "
        pdb=" C   HIS A  64 "
      ideal   model   delta    sigma   weight residual
     110.06  102.44    7.62 1.43e+00 4.89e-01 2.84e+01
  ... (remaining 11427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4581
       17.53 -    35.07: 362
       35.07 -    52.60: 66
       52.60 -    70.14: 14
       70.14 -    87.67: 3
  Dihedral angle restraints: 5026
    sinusoidal: 1979
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 182 "
           pdb=" CB  CYS R 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.74  -86.74     1      1.00e+01 1.00e-02 9.05e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.94  -67.94     1      1.00e+01 1.00e-02 5.99e+01
  dihedral pdb=" C   CYS N  96 "
           pdb=" N   CYS N  96 "
           pdb=" CA  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.09  -13.51     0      2.50e+00 1.60e-01 2.92e+01
  ... (remaining 5023 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1025
       0.059 -    0.117: 200
       0.117 -    0.176: 36
       0.176 -    0.234: 8
       0.234 -    0.293: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  LYS A 126 "
            pdb=" N   LYS A 126 "
            pdb=" C   LYS A 126 "
            pdb=" CB  LYS A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  MET A  60 "
            pdb=" N   MET A  60 "
            pdb=" C   MET A  60 "
            pdb=" CB  MET A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  GLU R 162 "
            pdb=" N   GLU R 162 "
            pdb=" C   GLU R 162 "
            pdb=" CB  GLU R 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR N  94 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.91e+00
        pdb=" C   TYR N  94 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR N  94 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYR N  95 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  57 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.19e+00
        pdb=" C   LYS B  57 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LYS B  57 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE B  58 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 125 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   PHE A 125 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE A 125 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 126 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2228
        2.80 -     3.33: 7744
        3.33 -     3.85: 14024
        3.85 -     4.38: 16667
        4.38 -     4.90: 29104
  Nonbonded interactions: 69767
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  90 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OH  TYR B  59 "
            pdb=" OE1 GLN B  75 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.320 3.040
  ... (remaining 69762 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.360
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   8441  Z= 0.340
  Angle     :  0.712  11.611  11432  Z= 0.428
  Chirality :  0.053   0.293   1275
  Planarity :  0.004   0.039   1456
  Dihedral  : 12.995  87.674   3049
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  1.12 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.10 %
  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:  0.81 (0.27), residues: 1033
  helix:  2.09 (0.26), residues: 409
  sheet: -0.20 (0.35), residues: 213
  loop : -0.61 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R  89 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.027   0.002   PHE R 185 
 TYR   0.016   0.001   TYR N  60 
 ARG   0.003   0.000   ARG N 118 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.860 
Fit side-chains
REVERT: N    3 GLN cc_start: 0.8194 (pt0) cc_final: 0.7623 (pt0)
REVERT: R   60 TRP cc_start: 0.8292 (m100) cc_final: 0.8079 (m100)
  outliers start: 8
  outliers final: 2
  residues processed: 174
  average time/residue: 1.2039
  time to fit residues: 222.5572
Evaluate side-chains
  132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue  225 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.1980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 130 ASN
A 146 GLN
G  24 ASN
R 300 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.150798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111128 restraints weight = 9618.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.41
r_work: 0.3193 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8441  Z= 0.209
  Angle     :  0.526   6.381  11432  Z= 0.281
  Chirality :  0.042   0.134   1275
  Planarity :  0.004   0.038   1456
  Dihedral  :  4.898  43.499   1160
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.74 %
    Favored  : 86.02 %
  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:  0.99 (0.27), residues: 1033
  helix:  2.35 (0.26), residues: 409
  sheet: -0.18 (0.37), residues: 193
  loop : -0.58 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.012   0.001   TYR R 279 
 ARG   0.005   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.902 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7629 (ttp-110)
REVERT: N    3 GLN cc_start: 0.8182 (pt0) cc_final: 0.7485 (pt0)
REVERT: R  188 LYS cc_start: 0.8447 (mmtp) cc_final: 0.8170 (mmtp)
  outliers start: 20
  outliers final: 8
  residues processed: 147
  average time/residue: 1.2987
  time to fit residues: 202.5955
Evaluate side-chains
  131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0370
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.152701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.112833 restraints weight = 9831.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.45
r_work: 0.3219 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8441  Z= 0.151
  Angle     :  0.479   6.988  11432  Z= 0.253
  Chirality :  0.041   0.148   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.268  24.679   1158
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.42 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.10 (0.27), residues: 1033
  helix:  2.45 (0.26), residues: 411
  sheet: -0.22 (0.36), residues: 197
  loop : -0.49 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.011   0.001   PHE R 165 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG N  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.897 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8470 (m-80) cc_final: 0.8211 (m-80)
REVERT: N    3 GLN cc_start: 0.8168 (pt0) cc_final: 0.7494 (pt0)
REVERT: R   83 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6044 (ttm170)
REVERT: R  188 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8188 (mmtp)
  outliers start: 20
  outliers final: 12
  residues processed: 145
  average time/residue: 1.2180
  time to fit residues: 187.9033
Evaluate side-chains
  132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0030
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.152011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112243 restraints weight = 9691.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.42
r_work: 0.3186 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8441  Z= 0.172
  Angle     :  0.492   8.766  11432  Z= 0.257
  Chirality :  0.041   0.139   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.213  24.573   1158
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.32 %
    Favored  : 81.88 %
  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:  1.14 (0.27), residues: 1033
  helix:  2.54 (0.26), residues: 408
  sheet: -0.18 (0.36), residues: 190
  loop : -0.53 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.010   0.001   PHE R 267 
 TYR   0.011   0.001   TYR R 308 
 ARG   0.005   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.904 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7687 (ttp-110)
REVERT: B  217 MET cc_start: 0.7591 (ptt) cc_final: 0.7341 (pmt)
REVERT: G   21 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (mpp)
REVERT: N    3 GLN cc_start: 0.8168 (pt0) cc_final: 0.7531 (pt0)
REVERT: R   83 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6033 (ttm170)
  outliers start: 25
  outliers final: 12
  residues processed: 138
  average time/residue: 1.2452
  time to fit residues: 182.9459
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.149164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111896 restraints weight = 9703.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.28
r_work: 0.3208 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8441  Z= 0.193
  Angle     :  0.498   9.168  11432  Z= 0.259
  Chirality :  0.042   0.139   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.221  24.499   1158
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.33 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1033
  helix:  2.52 (0.26), residues: 410
  sheet: -0.15 (0.36), residues: 193
  loop : -0.52 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.011   0.001   PHE R 267 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.003   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.848 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7685 (ttp-110)
REVERT: B  217 MET cc_start: 0.7527 (ptt) cc_final: 0.7289 (pmt)
REVERT: G   17 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8455 (mp0)
REVERT: G   21 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8506 (mpp)
REVERT: N    3 GLN cc_start: 0.8139 (pt0) cc_final: 0.7502 (pt0)
REVERT: R   83 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6017 (ttm170)
  outliers start: 29
  outliers final: 15
  residues processed: 144
  average time/residue: 1.1583
  time to fit residues: 178.0006
Evaluate side-chains
  132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.0370
   chunk 57 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N   5 GLN
R 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114055 restraints weight = 9685.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.29
r_work: 0.3207 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8441  Z= 0.155
  Angle     :  0.488   9.968  11432  Z= 0.254
  Chirality :  0.041   0.191   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.080  24.013   1158
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.44 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.21 (0.27), residues: 1033
  helix:  2.56 (0.26), residues: 410
  sheet: -0.04 (0.36), residues: 196
  loop : -0.51 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.010   0.001   PHE R 267 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.003   0.000   ARG N  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7418 (tt0) cc_final: 0.6939 (mt-10)
REVERT: B  217 MET cc_start: 0.7543 (ptt) cc_final: 0.7311 (pmt)
REVERT: G   17 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8473 (mp0)
REVERT: G   21 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8504 (mpp)
REVERT: N    3 GLN cc_start: 0.8094 (pt0) cc_final: 0.7410 (pt0)
REVERT: N   85 SER cc_start: 0.8685 (m) cc_final: 0.8304 (p)
REVERT: R   83 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.5922 (ttm170)
  outliers start: 30
  outliers final: 15
  residues processed: 144
  average time/residue: 1.1436
  time to fit residues: 176.2948
Evaluate side-chains
  137 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.149207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.111533 restraints weight = 9778.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.30
r_work: 0.3168 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8441  Z= 0.220
  Angle     :  0.526  11.079  11432  Z= 0.273
  Chirality :  0.043   0.166   1275
  Planarity :  0.003   0.048   1456
  Dihedral  :  4.246  24.400   1158
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.01 %
    Favored  : 79.31 %
  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:  1.16 (0.27), residues: 1033
  helix:  2.49 (0.26), residues: 410
  sheet: -0.17 (0.36), residues: 205
  loop : -0.45 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.012   0.001   PHE R 267 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.011   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.963 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7682 (ttp-110)
REVERT: B  217 MET cc_start: 0.7535 (ptt) cc_final: 0.7297 (pmt)
REVERT: G   17 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8479 (mp0)
REVERT: N    3 GLN cc_start: 0.8089 (pt0) cc_final: 0.7435 (pt0)
REVERT: R   83 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5948 (ttm170)
  outliers start: 24
  outliers final: 17
  residues processed: 135
  average time/residue: 1.2395
  time to fit residues: 178.3050
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.108582 restraints weight = 9800.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.44
r_work: 0.3132 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8441  Z= 0.267
  Angle     :  0.540   7.608  11432  Z= 0.283
  Chirality :  0.043   0.165   1275
  Planarity :  0.004   0.047   1456
  Dihedral  :  4.417  24.742   1158
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.12 %
    Favored  : 79.08 %
  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:  1.07 (0.27), residues: 1033
  helix:  2.49 (0.26), residues: 404
  sheet: -0.26 (0.36), residues: 197
  loop : -0.51 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.014   0.002   PHE B 292 
 TYR   0.015   0.002   TYR N  80 
 ARG   0.010   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8087 (ttm110)
REVERT: B   19 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7635 (ttp-110)
REVERT: B  217 MET cc_start: 0.7589 (ptt) cc_final: 0.7354 (pmt)
REVERT: G   17 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8505 (mp0)
REVERT: G   58 GLU cc_start: 0.7836 (tp30) cc_final: 0.7603 (tp30)
REVERT: N    3 GLN cc_start: 0.8151 (pt0) cc_final: 0.7532 (pt0)
REVERT: R   83 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6038 (ttm170)
REVERT: R   88 CYS cc_start: 0.8098 (t) cc_final: 0.7540 (t)
  outliers start: 25
  outliers final: 14
  residues processed: 138
  average time/residue: 1.2189
  time to fit residues: 179.1692
Evaluate side-chains
  130 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108933 restraints weight = 9875.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.45
r_work: 0.3138 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8441  Z= 0.245
  Angle     :  0.556  12.826  11432  Z= 0.285
  Chirality :  0.043   0.156   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.392  25.041   1158
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.24 %
    Favored  : 78.52 %
  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:  1.00 (0.27), residues: 1033
  helix:  2.37 (0.26), residues: 410
  sheet: -0.22 (0.36), residues: 197
  loop : -0.58 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.013   0.001   PHE B 292 
 TYR   0.013   0.001   TYR R 308 
 ARG   0.009   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A  132 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (ttm110)
REVERT: B   19 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7647 (ttp-110)
REVERT: G   17 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8483 (mp0)
REVERT: G   21 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8289 (mpp)
REVERT: G   58 GLU cc_start: 0.7829 (tp30) cc_final: 0.7592 (tp30)
REVERT: N    3 GLN cc_start: 0.8146 (pt0) cc_final: 0.7527 (pt0)
REVERT: N  120 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8269 (mm-40)
REVERT: R   83 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6030 (ttm170)
  outliers start: 20
  outliers final: 12
  residues processed: 132
  average time/residue: 1.3201
  time to fit residues: 184.6718
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ARG
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.111493 restraints weight = 9745.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.30
r_work: 0.3194 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8441  Z= 0.193
  Angle     :  0.523  10.476  11432  Z= 0.270
  Chirality :  0.042   0.153   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.296  25.240   1158
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.57 %
    Favored  : 78.41 %
  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:  1.10 (0.27), residues: 1033
  helix:  2.42 (0.26), residues: 410
  sheet: -0.18 (0.36), residues: 205
  loop : -0.47 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.009   0.000   ARG B  19 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.929 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7630 (ttp-110)
REVERT: B  217 MET cc_start: 0.7531 (ptt) cc_final: 0.7273 (pmt)
REVERT: G   17 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8518 (mp0)
REVERT: G   21 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8262 (mpp)
REVERT: N    3 GLN cc_start: 0.8115 (pt0) cc_final: 0.7479 (pt0)
REVERT: N  120 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8207 (mm-40)
REVERT: R   83 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.5967 (ttm170)
  outliers start: 18
  outliers final: 11
  residues processed: 130
  average time/residue: 1.2330
  time to fit residues: 170.6138
Evaluate side-chains
  130 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  290 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0970
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.151110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110745 restraints weight = 9766.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.44
r_work: 0.3163 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8441  Z= 0.189
  Angle     :  0.526  10.477  11432  Z= 0.271
  Chirality :  0.042   0.149   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.252  25.206   1158
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.47 %
    Favored  : 77.85 %
  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:  1.14 (0.27), residues: 1033
  helix:  2.43 (0.26), residues: 410
  sheet: -0.13 (0.36), residues: 205
  loop : -0.45 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.008   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6608.45 seconds
wall clock time: 117 minutes 19.27 seconds (7039.27 seconds total)