Starting phenix.real_space_refine
on Fri Dec  8 11:48:00 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_ligands.cif

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 {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/12_2023/8w8a_37350_updated.pdb"
  }
  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
    Residue "A ARG   61": "NH1" <-> "NH2"
    Residue "A GLU  179": "OE1" <-> "OE2"
    Residue "A GLU  182": "OE1" <-> "OE2"
    Residue "A GLU  222": "OE1" <-> "OE2"
    Residue "A GLU  244": "OE1" <-> "OE2"
    Residue "R ARG   83": "NH1" <-> "NH2"
    Residue "R TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  162": "OE1" <-> "OE2"
    Residue "R PHE  276": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.76, per 1000 atoms: 0.58
  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  - 3.50
        Amino acid           : False - 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: 3.10
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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...
  running ksdssp...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      39.4% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 36
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 160 through 163
      No H-bonds generated for 'chain 'A' and resid 160 through 163'
    Processing helix  chain 'A' and resid 165 through 167
      No H-bonds generated for 'chain 'A' and resid 165 through 167'
    Processing helix  chain 'A' and resid 184 through 204
      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 223 through 242
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 4.915A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'R' and resid 20 through 50
    Processing helix  chain 'R' and resid 57 through 75
    Processing helix  chain 'R' and resid 77 through 85
      removed outlier: 3.685A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 93 through 126
    Processing helix  chain 'R' and resid 128 through 134
      removed outlier: 3.706A  pdb=" N   TYR R 131 " --> pdb=" O   PRO R 128 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   LYS R 132 " --> pdb=" O   LEU R 129 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS R 134 " --> pdb=" O   TYR R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 159
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 169 through 179
    Processing helix  chain 'R' and resid 188 through 198
      removed outlier: 3.562A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 231
    Processing helix  chain 'R' and resid 248 through 275
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 277 through 279
      No H-bonds generated for 'chain 'R' and resid 277 through 279'
    Processing helix  chain 'R' and resid 283 through 305
      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 309 through 317
    Processing sheet with id=  A, first strand: chain 'A' and resid 138 through 144
      removed outlier: 4.132A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ASN A  80 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   HIS A  82 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 8.772A  pdb=" N   VAL A  86 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.819A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (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=  C, 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=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.654A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (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=  E, 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=  F, 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=  G, first strand: chain 'B' and resid 306 through 308
    Processing sheet with id=  H, 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=  I, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.320A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'N' and resid 18 through 20

    396 hydrogen bonds defined for protein.
    1137 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: 2.34

  Time building geometry restraints manager: 3.34 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=" C13 T5U R 401 "
       pdb=" O01 T5U R 401 "
    ideal  model  delta    sigma   weight residual
    1.536  1.375  0.161 2.00e-02 2.50e+03 6.51e+01
  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=" C09 T5U R 401 "
       pdb=" O01 T5U R 401 "
    ideal  model  delta    sigma   weight residual
    1.308  1.405 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" C13 T5U R 401 "
       pdb=" N03 T5U R 401 "
    ideal  model  delta    sigma   weight residual
    1.267  1.354 -0.087 2.00e-02 2.50e+03 1.90e+01
  ... (remaining 8436 not shown)

  Histogram of bond angle deviations from ideal:
       99.91 -   107.25: 273
      107.25 -   114.59: 4896
      114.59 -   121.93: 4598
      121.93 -   129.27: 1596
      129.27 -   136.61: 69
  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: 4576
       17.53 -    35.07: 358
       35.07 -    52.60: 66
       52.60 -    70.14: 14
       70.14 -    87.67: 3
  Dihedral angle restraints: 5017
    sinusoidal: 1970
      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 5014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1024
       0.059 -    0.117: 200
       0.117 -    0.176: 36
       0.176 -    0.234: 9
       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: 2229
        2.80 -     3.33: 7785
        3.33 -     3.85: 14077
        3.85 -     4.38: 16729
        4.38 -     4.90: 29103
  Nonbonded interactions: 69923
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  90 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.280 2.520
  nonbonded pdb=" OH  TYR B  59 "
            pdb=" OE1 GLN B  75 "
     model   vdw
     2.290 2.440
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.292 2.440
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.303 2.440
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.320 2.440
  ... (remaining 69918 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.350
  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:          6.010
  Check model and map are aligned:         0.120
  Set scattering table:                    0.090
  Process input model:                     25.500
  Find NCS groups from input model:        0.250
  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:             0.010
  Load rotamer database and sin/cos tables:12.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.160
-------------------------------------------------------------------------------
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      :  0.006   0.161   8441  Z= 0.400
  Angle     :  0.725  11.611  11432  Z= 0.430
  Chirality :  0.053   0.293   1275
  Planarity :  0.004   0.039   1456
  Dihedral  : 12.966  87.674   3040
  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 fitting.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.915 
Fit side-chains
  outliers start: 8
  outliers final: 2
  residues processed: 174
  average time/residue: 1.1362
  time to fit residues: 210.8265
Evaluate side-chains
  133 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.931 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 2
  residues processed: 0
  time to fit residues: 1.2703
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 58 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.8104

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8441  Z= 0.338
  Angle     :  0.573   6.734  11432  Z= 0.301
  Chirality :  0.045   0.167   1275
  Planarity :  0.004   0.037   1456
  Dihedral  :  4.820  48.649   1149
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 10.85 %
    Favored  : 85.68 %
  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:  0.80 (0.26), residues: 1033
  helix:  2.14 (0.26), residues: 409
  sheet: -0.29 (0.36), residues: 193
  loop : -0.63 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B 169 
   HIS   0.007   0.001   HIS A 209 
   PHE   0.015   0.002   PHE B 292 
   TYR   0.013   0.002   TYR R 308 
   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
  162 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.949 
Fit side-chains
  outliers start: 31
  outliers final: 15
  residues processed: 145
  average time/residue: 1.1432
  time to fit residues: 176.8161
Evaluate side-chains
  136 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.997 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 8
  residues processed: 8
  average time/residue: 0.2880
  time to fit residues: 4.1138
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8441  Z= 0.231
  Angle     :  0.517   9.610  11432  Z= 0.269
  Chirality :  0.043   0.162   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.496  48.316   1149
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.54 %
    Favored  : 83.00 %
  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:  0.86 (0.26), residues: 1033
  helix:  2.21 (0.26), residues: 410
  sheet: -0.30 (0.35), residues: 194
  loop : -0.59 (0.30), residues: 429

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   0.012   0.001   PHE B 292 
   TYR   0.013   0.001   TYR R 308 
   ARG   0.005   0.000   ARG B  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 fitting.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.890 
Fit side-chains
  outliers start: 22
  outliers final: 13
  residues processed: 142
  average time/residue: 1.1815
  time to fit residues: 178.8089
Evaluate side-chains
  137 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.858 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 8
  residues processed: 5
  average time/residue: 0.1941
  time to fit residues: 2.5035
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 92 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 81 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
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8441  Z= 0.195
  Angle     :  0.493   8.255  11432  Z= 0.256
  Chirality :  0.042   0.156   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.370  49.273   1149
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.99 %
    Favored  : 81.66 %
  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 (0.26), residues: 1033
  helix:  2.38 (0.26), residues: 404
  sheet: -0.20 (0.36), residues: 192
  loop : -0.56 (0.29), residues: 437

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   0.012   0.001   PHE R 165 
   TYR   0.014   0.001   TYR R  90 
   ARG   0.007   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
  163 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.955 
Fit side-chains
  outliers start: 30
  outliers final: 16
  residues processed: 147
  average time/residue: 1.1680
  time to fit residues: 183.2035
Evaluate side-chains
  137 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.935 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 8
  residues processed: 8
  average time/residue: 0.1575
  time to fit residues: 3.1201
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 1 optimal weight:    0.2980
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
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   0.026   8441  Z= 0.151
  Angle     :  0.477   8.361  11432  Z= 0.247
  Chirality :  0.041   0.191   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.242  48.837   1149
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.79 %
    Favored  : 79.42 %
  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:  1.11 (0.26), residues: 1033
  helix:  2.50 (0.26), residues: 404
  sheet: -0.20 (0.34), residues: 213
  loop : -0.51 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP R  89 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.014   0.001   PHE R  91 
   TYR   0.012   0.001   TYR R 308 
   ARG   0.007   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
  157 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.935 
Fit side-chains
  outliers start: 25
  outliers final: 12
  residues processed: 145
  average time/residue: 1.1828
  time to fit residues: 182.8944
Evaluate side-chains
  130 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 1.000 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 8
  residues processed: 4
  average time/residue: 0.1482
  time to fit residues: 2.2631
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.3980
   chunk 19 optimal weight:    0.4980
   chunk 57 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.3980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8441  Z= 0.150
  Angle     :  0.488  11.528  11432  Z= 0.247
  Chirality :  0.041   0.162   1275
  Planarity :  0.003   0.041   1456
  Dihedral  :  4.198  48.226   1149
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.68 %
    Favored  : 78.64 %
  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:  1.25 (0.26), residues: 1033
  helix:  2.66 (0.26), residues: 401
  sheet: -0.11 (0.34), residues: 212
  loop : -0.46 (0.30), residues: 420

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   0.009   0.001   PHE B 151 
   TYR   0.017   0.001   TYR N  80 
   ARG   0.012   0.000   ARG A 199 

*********************** 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
  150 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.948 
Fit side-chains
  outliers start: 24
  outliers final: 14
  residues processed: 138
  average time/residue: 1.1934
  time to fit residues: 175.6749
Evaluate side-chains
  129 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 1.000 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 9
  residues processed: 5
  average time/residue: 0.1357
  time to fit residues: 2.2609
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0370
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0060
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0000
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.5280

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1851

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= 0.147
  Angle     :  0.488  10.288  11432  Z= 0.247
  Chirality :  0.041   0.156   1275
  Planarity :  0.003   0.047   1456
  Dihedral  :  4.130  47.604   1149
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.35 %
    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:  1.31 (0.27), residues: 1033
  helix:  2.66 (0.26), residues: 403
  sheet: -0.10 (0.35), residues: 206
  loop : -0.38 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP B 169 
   HIS   0.003   0.000   HIS R  63 
   PHE   0.012   0.001   PHE R  91 
   TYR   0.011   0.001   TYR R 308 
   ARG   0.012   0.000   ARG A 199 

*********************** 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
  144 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.968 
Fit side-chains
  outliers start: 19
  outliers final: 12
  residues processed: 138
  average time/residue: 1.1293
  time to fit residues: 166.8750
Evaluate side-chains
  135 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 9
  residues processed: 3
  average time/residue: 0.1442
  time to fit residues: 1.9787
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  82 GLN
R 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8441  Z= 0.191
  Angle     :  0.495   9.940  11432  Z= 0.253
  Chirality :  0.042   0.156   1275
  Planarity :  0.003   0.047   1456
  Dihedral  :  4.206  48.045   1149
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.13 %
    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:  1.29 (0.27), residues: 1033
  helix:  2.65 (0.26), residues: 403
  sheet: -0.18 (0.33), residues: 228
  loop : -0.33 (0.31), residues: 402

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   0.010   0.001   PHE B 292 
   TYR   0.012   0.001   TYR R 308 
   ARG   0.010   0.000   ARG A 199 

*********************** 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
  147 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.962 
Fit side-chains
  outliers start: 23
  outliers final: 14
  residues processed: 137
  average time/residue: 1.2650
  time to fit residues: 185.8803
Evaluate side-chains
  129 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.944 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 9
  residues processed: 5
  average time/residue: 0.1624
  time to fit residues: 2.4632
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 93 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8441  Z= 0.175
  Angle     :  0.504   9.844  11432  Z= 0.255
  Chirality :  0.042   0.155   1275
  Planarity :  0.003   0.041   1456
  Dihedral  :  4.188  47.562   1149
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.80 %
    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:  1.28 (0.27), residues: 1033
  helix:  2.67 (0.26), residues: 403
  sheet: -0.24 (0.33), residues: 232
  loop : -0.35 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP R  89 
   HIS   0.004   0.001   HIS A 209 
   PHE   0.013   0.001   PHE R  91 
   TYR   0.012   0.001   TYR N  80 
   ARG   0.009   0.000   ARG A 199 

*********************** 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
  136 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.779 
Fit side-chains
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 1.1129
  time to fit residues: 157.3285
Evaluate side-chains
  128 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 10
  residues processed: 2
  average time/residue: 0.6218
  time to fit residues: 2.6990
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 80 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8441  Z= 0.181
  Angle     :  0.514  13.448  11432  Z= 0.256
  Chirality :  0.042   0.155   1275
  Planarity :  0.003   0.040   1456
  Dihedral  :  4.198  47.282   1149
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 20.58 %
    Favored  : 77.96 %
  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:  1.26 (0.27), residues: 1033
  helix:  2.64 (0.26), residues: 403
  sheet: -0.24 (0.33), residues: 232
  loop : -0.34 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP R  89 
   HIS   0.004   0.001   HIS A 209 
   PHE   0.009   0.001   PHE B 292 
   TYR   0.012   0.001   TYR R 308 
   ARG   0.010   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
  134 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.914 
Fit side-chains
  outliers start: 13
  outliers final: 11
  residues processed: 134
  average time/residue: 1.1200
  time to fit residues: 160.6271
Evaluate side-chains
  130 residues out of total 900 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 1.021 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 11
  residues processed: 0
  time to fit residues: 1.4019
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.1784

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

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

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 = 0.149102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.109113 restraints weight = 9678.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.41
r_work: 0.3165 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8441  Z= 0.236
  Angle     :  0.534  12.496  11432  Z= 0.269
  Chirality :  0.043   0.155   1275
  Planarity :  0.003   0.041   1456
  Dihedral  :  4.323  48.089   1149
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.02 %
    Favored  : 78.08 %
  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:  1.19 (0.27), residues: 1033
  helix:  2.57 (0.26), residues: 402
  sheet: -0.22 (0.33), residues: 230
  loop : -0.40 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP R  89 
   HIS   0.005   0.001   HIS R  63 
   PHE   0.014   0.001   PHE R  91 
   TYR   0.012   0.001   TYR R 308 
   ARG   0.009   0.000   ARG A 199 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3476.59 seconds
wall clock time: 62 minutes 31.23 seconds (3751.23 seconds total)