Starting phenix.real_space_refine
on Fri Dec  8 22:49:06 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/12_2023/7vuh_32128_updated.pdb"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     Cl      1      4.86       5
     C    5292      2.51       5
     N    1436      2.21       5
     O    1523      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R TYR  253": "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: 8302
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1970
          Classifications: {'peptide': 239}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    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: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 2335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2335
          Unusual residues: {'7ZQ': 1}
          Classifications: {'peptide': 282, 'undetermined': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 269, None: 1}
            Not linked:
              pdbres="PHE R 304 "
              pdbres="7ZQ R 401 "
  Time building chain proxies: 4.97, per 1000 atoms: 0.60
  Number of scatterers: 8302
  At special positions: 0
  Unit cell: (76.96, 99.84, 134.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      50     16.00
     O    1523      8.00
     N    1436      7.00
     C    5292      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  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: 3.46
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 11 sheets defined
      35.5% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 37
      removed outlier: 3.734A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 62
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 284 through 293
    Processing helix  chain 'A' and resid 298 through 301
      No H-bonds generated for 'chain 'A' and resid 298 through 301'
    Processing helix  chain 'A' and resid 322 through 341
      removed outlier: 3.649A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ALA A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 380
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 74 through 76
      No H-bonds generated for 'chain 'N' and resid 74 through 76'
    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 24 through 53
      Proline residue:  R  29  - end of helix
      Proline residue:  R  42  - end of helix
      removed outlier: 3.843A  pdb=" N   GLN R  53 " --> pdb=" O   ILE R  49 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 55 through 58
      removed outlier: 3.614A  pdb=" N   ARG R  58 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 55 through 58'
    Processing helix  chain 'R' and resid 61 through 82
      removed outlier: 3.844A  pdb=" N   VAL R  81 " --> pdb=" O   LEU R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 90
      No H-bonds generated for 'chain 'R' and resid 87 through 90'
    Processing helix  chain 'R' and resid 102 through 131
      removed outlier: 3.594A  pdb=" N   LEU R 107 " --> pdb=" O   ILE R 103 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 144 through 159
      removed outlier: 3.645A  pdb=" N   VAL R 152 " --> pdb=" O   VAL R 148 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   TYR R 153 " --> pdb=" O   ILE R 149 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE R 154 " --> pdb=" O   VAL R 150 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR R 155 " --> pdb=" O   SER R 151 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 191
    Processing helix  chain 'R' and resid 193 through 211
      removed outlier: 4.003A  pdb=" N   LEU R 202 " --> pdb=" O   ILE R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 227 through 253
      removed outlier: 4.214A  pdb=" N   THR R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE R 237 " --> pdb=" O   ILE R 233 " (cutoff:3.500A)
      Proline residue:  R 243  - end of helix
      removed outlier: 3.955A  pdb=" N   LEU R 252 " --> pdb=" O   ILE R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 261
      No H-bonds generated for 'chain 'R' and resid 259 through 261'
    Processing helix  chain 'R' and resid 263 through 283
      removed outlier: 3.686A  pdb=" N   THR R 278 " --> pdb=" O   ALA R 274 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA R 279 " --> pdb=" O   LEU R 275 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   PHE R 282 " --> pdb=" O   THR R 278 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE R 283 " --> pdb=" O   ALA R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 290 through 299
    Processing sheet with id=  A, first strand: chain 'A' and resid 349 through 353
      removed outlier: 6.895A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   HIS A 352 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 279 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   HIS A 220 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.080A  pdb=" N   VAL A 224 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.064A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.478A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.438A  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 150
      removed outlier: 6.629A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 189 through 191
      removed outlier: 3.554A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.415A  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: 6.612A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 294 through 298
    Processing sheet with id=  H, first strand: chain 'B' and resid 327 through 330
      removed outlier: 3.655A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.570A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'N' and resid 18 through 20
      removed outlier: 3.719A  pdb=" N   THR N  78 " --> pdb=" O   ASP N  73 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'N' and resid 95 through 98
      removed outlier: 3.677A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    329 hydrogen bonds defined for protein.
    963 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: 2.31

  Time building geometry restraints manager: 3.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1334
        1.31 -     1.44: 2377
        1.44 -     1.56: 4700
        1.56 -     1.69: 0
        1.69 -     1.82: 71
  Bond restraints: 8482
  Sorted by residual:
  bond pdb=" C9  7ZQ R 401 "
       pdb=" N2  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.341  1.447 -0.106 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C7  7ZQ R 401 "
       pdb=" N1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.448 -0.104 2.00e-02 2.50e+03 2.72e+01
  bond pdb=" C3  7ZQ R 401 "
       pdb="CL1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.732  1.784 -0.052 2.00e-02 2.50e+03 6.72e+00
  bond pdb=" C7  7ZQ R 401 "
       pdb=" O1  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.222  1.182  0.040 2.00e-02 2.50e+03 3.95e+00
  bond pdb=" C9  7ZQ R 401 "
       pdb=" O2  7ZQ R 401 "
    ideal  model  delta    sigma   weight residual
    1.219  1.180  0.039 2.00e-02 2.50e+03 3.77e+00
  ... (remaining 8477 not shown)

  Histogram of bond angle deviations from ideal:
       98.73 -   105.78: 137
      105.78 -   112.84: 4503
      112.84 -   119.89: 2865
      119.89 -   126.95: 3896
      126.95 -   134.00: 101
  Bond angle restraints: 11502
  Sorted by residual:
  angle pdb=" N   ILE R 118 "
        pdb=" CA  ILE R 118 "
        pdb=" C   ILE R 118 "
      ideal   model   delta    sigma   weight residual
     111.81  107.53    4.28 8.60e-01 1.35e+00 2.47e+01
  angle pdb=" C   SER R 160 "
        pdb=" N   ILE R 161 "
        pdb=" CA  ILE R 161 "
      ideal   model   delta    sigma   weight residual
     120.24  122.90   -2.66 6.30e-01 2.52e+00 1.79e+01
  angle pdb=" C   VAL R 191 "
        pdb=" N   TYR R 192 "
        pdb=" CA  TYR R 192 "
      ideal   model   delta    sigma   weight residual
     122.17  116.39    5.78 1.54e+00 4.22e-01 1.41e+01
  angle pdb=" C   PHE R  27 "
        pdb=" N   VAL R  28 "
        pdb=" CA  VAL R  28 "
      ideal   model   delta    sigma   weight residual
     120.24  122.30   -2.06 6.30e-01 2.52e+00 1.07e+01
  angle pdb=" N   GLY B 116 "
        pdb=" CA  GLY B 116 "
        pdb=" C   GLY B 116 "
      ideal   model   delta    sigma   weight residual
     111.56  114.56   -3.00 1.01e+00 9.80e-01 8.84e+00
  ... (remaining 11497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 4568
       17.34 -    34.69: 384
       34.69 -    52.03: 74
       52.03 -    69.38: 8
       69.38 -    86.72: 12
  Dihedral angle restraints: 5046
    sinusoidal: 1999
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -29.67  -56.33     1      1.00e+01 1.00e-02 4.28e+01
  dihedral pdb=" CA  ASN R 168 "
           pdb=" C   ASN R 168 "
           pdb=" N   ILE R 169 "
           pdb=" CA  ILE R 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.36  -19.64     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  TRP R 117 "
           pdb=" C   TRP R 117 "
           pdb=" N   ILE R 118 "
           pdb=" CA  ILE R 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.69   19.31     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 5043 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 798
       0.033 -    0.065: 327
       0.065 -    0.098: 115
       0.098 -    0.130: 53
       0.130 -    0.163: 6
  Chirality restraints: 1299
  Sorted by residual:
  chirality pdb=" CA  LYS A 283 "
            pdb=" N   LYS A 283 "
            pdb=" C   LYS A 283 "
            pdb=" CB  LYS A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.64e-01
  chirality pdb=" CB  ILE R 104 "
            pdb=" CA  ILE R 104 "
            pdb=" CG1 ILE R 104 "
            pdb=" CG2 ILE R 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CG  LEU A  46 "
            pdb=" CB  LEU A  46 "
            pdb=" CD1 LEU A  46 "
            pdb=" CD2 LEU A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 1296 not shown)

  Planarity restraints: 1459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R  82 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.33e+00
        pdb=" C   PHE R  82 "    0.040 2.00e-02 2.50e+03
        pdb=" O   PHE R  82 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL R  83 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 141 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO R 142 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 142 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 142 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  87 "   -0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   LEU R  87 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU R  87 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU R  88 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1456 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 152
        2.66 -     3.22: 8202
        3.22 -     3.78: 13218
        3.78 -     4.34: 18392
        4.34 -     4.90: 29777
  Nonbonded interactions: 69741
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 308 "
            pdb=" OD2 ASP A 333 "
     model   vdw
     2.099 2.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.131 2.440
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.137 2.440
  nonbonded pdb=" OD1 ASP A 249 "
            pdb=" NZ  LYS A 283 "
     model   vdw
     2.163 2.520
  nonbonded pdb=" OD2 ASP B  27 "
            pdb=" OG  SER G  31 "
     model   vdw
     2.197 2.440
  ... (remaining 69736 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.790
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.710
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
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      :  0.004   0.106   8482  Z= 0.240
  Angle     :  0.656   7.796  11502  Z= 0.364
  Chirality :  0.044   0.163   1299
  Planarity :  0.004   0.051   1459
  Dihedral  : 13.682  86.724   3070
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -1.87 (0.26), residues: 1030
  helix:  0.32 (0.28), residues: 380
  sheet: -2.64 (0.33), residues: 182
  loop : -1.94 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.004   0.001   HIS B 225 
   PHE   0.020   0.002   PHE R  79 
   TYR   0.015   0.001   TYR R 253 
   ARG   0.010   0.000   ARG A 379 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2383
  time to fit residues: 65.5903
Evaluate side-chains
  201 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.822 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3570
-------------------------------------------------------------------------------
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:    0.0000
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B 340 ASN
G  59 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8482  Z= 0.243
  Angle     :  0.586   8.477  11502  Z= 0.307
  Chirality :  0.044   0.181   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.414  51.285   1155
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.65 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.26), residues: 1030
  helix:  0.57 (0.29), residues: 375
  sheet: -2.09 (0.33), residues: 184
  loop : -1.84 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.003   0.001   HIS R 181 
   PHE   0.015   0.002   PHE R 282 
   TYR   0.018   0.002   TYR R 253 
   ARG   0.004   0.000   ARG A 363 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 0.970 
Fit side-chains
  outliers start: 15
  outliers final: 15
  residues processed: 202
  average time/residue: 0.2487
  time to fit residues: 67.0815
Evaluate side-chains
  204 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 189
  time to evaluate  : 0.914 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 0
  residues processed: 15
  average time/residue: 0.1014
  time to fit residues: 3.8736
-------------------------------------------------------------------------------
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:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0270
   chunk 62 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
G  44 HIS
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8482  Z= 0.209
  Angle     :  0.551   5.477  11502  Z= 0.291
  Chirality :  0.042   0.182   1299
  Planarity :  0.004   0.052   1459
  Dihedral  :  5.229  47.464   1155
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.19 %
    Favored  : 85.48 %
  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: -1.36 (0.26), residues: 1030
  helix:  0.66 (0.29), residues: 374
  sheet: -1.94 (0.33), residues: 188
  loop : -1.73 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.003   0.001   HIS R 181 
   PHE   0.019   0.002   PHE A 330 
   TYR   0.019   0.001   TYR N  80 
   ARG   0.006   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 204
  time to evaluate  : 0.982 
Fit side-chains
  outliers start: 12
  outliers final: 6
  residues processed: 210
  average time/residue: 0.2328
  time to fit residues: 64.9155
Evaluate side-chains
  205 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 199
  time to evaluate  : 0.890 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0736
  time to fit residues: 2.0078
-------------------------------------------------------------------------------
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:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8482  Z= 0.275
  Angle     :  0.583  10.603  11502  Z= 0.307
  Chirality :  0.043   0.159   1299
  Planarity :  0.005   0.052   1459
  Dihedral  :  5.360  46.234   1155
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.96 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.26), residues: 1030
  helix:  0.66 (0.28), residues: 378
  sheet: -1.87 (0.33), residues: 197
  loop : -1.78 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP A 234 
   HIS   0.004   0.001   HIS R 181 
   PHE   0.026   0.002   PHE A 330 
   TYR   0.017   0.002   TYR R 253 
   ARG   0.007   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 211
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 12
  residues processed: 216
  average time/residue: 0.2352
  time to fit residues: 67.5378
Evaluate side-chains
  216 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 204
  time to evaluate  : 1.051 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0869
  time to fit residues: 3.3608
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 0 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8482  Z= 0.266
  Angle     :  0.587   9.998  11502  Z= 0.307
  Chirality :  0.043   0.191   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.546  47.385   1155
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.18 %
    Favored  : 79.82 %
  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 (0.26), residues: 1030
  helix:  0.70 (0.28), residues: 377
  sheet: -1.77 (0.34), residues: 201
  loop : -1.76 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.018   0.002   PHE R 282 
   TYR   0.020   0.002   TYR N  80 
   ARG   0.007   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 6
  residues processed: 200
  average time/residue: 0.2537
  time to fit residues: 67.0777
Evaluate side-chains
  195 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 189
  time to evaluate  : 0.882 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1463
  time to fit residues: 2.5807
-------------------------------------------------------------------------------
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:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 94 optimal weight:    0.6980
   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  44 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8482  Z= 0.276
  Angle     :  0.605  11.356  11502  Z= 0.313
  Chirality :  0.044   0.181   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.559  48.690   1155
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 18.63 %
    Favored  : 79.71 %
  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: -1.30 (0.26), residues: 1030
  helix:  0.68 (0.28), residues: 380
  sheet: -1.74 (0.34), residues: 205
  loop : -1.75 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP A 234 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.020   0.002   PHE R 282 
   TYR   0.018   0.002   TYR N  80 
   ARG   0.006   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 201
  time to evaluate  : 1.093 
Fit side-chains
  outliers start: 15
  outliers final: 11
  residues processed: 209
  average time/residue: 0.2330
  time to fit residues: 64.9364
Evaluate side-chains
  209 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 198
  time to evaluate  : 0.898 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0827
  time to fit residues: 2.9776
-------------------------------------------------------------------------------
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:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8482  Z= 0.239
  Angle     :  0.607   8.928  11502  Z= 0.311
  Chirality :  0.044   0.158   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.630  55.746   1155
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.62 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.26), residues: 1030
  helix:  0.68 (0.28), residues: 383
  sheet: -1.70 (0.34), residues: 200
  loop : -1.71 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.029   0.002   PHE A 330 
   TYR   0.017   0.002   TYR N  80 
   ARG   0.005   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.959 
Fit side-chains
  outliers start: 17
  outliers final: 10
  residues processed: 210
  average time/residue: 0.2441
  time to fit residues: 67.5776
Evaluate side-chains
  205 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 195
  time to evaluate  : 0.911 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0772
  time to fit residues: 2.8073
-------------------------------------------------------------------------------
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:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8482  Z= 0.264
  Angle     :  0.620   7.973  11502  Z= 0.319
  Chirality :  0.044   0.159   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.695  59.082   1155
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 20.40 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1030
  helix:  0.65 (0.28), residues: 388
  sheet: -1.74 (0.33), residues: 205
  loop : -1.72 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.029   0.002   PHE A 330 
   TYR   0.020   0.002   TYR N  80 
   ARG   0.004   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 202
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 206
  average time/residue: 0.2354
  time to fit residues: 64.6203
Evaluate side-chains
  211 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 205
  time to evaluate  : 0.919 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0806
  time to fit residues: 2.2453
-------------------------------------------------------------------------------
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:    0.0770
   chunk 54 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 95 optimal weight:    0.3980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8482  Z= 0.239
  Angle     :  0.612   7.607  11502  Z= 0.315
  Chirality :  0.043   0.161   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.650  59.784   1155
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 21.40 %
    Favored  : 77.72 %
  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: 1030
  helix:  0.60 (0.28), residues: 390
  sheet: -1.73 (0.34), residues: 205
  loop : -1.66 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.027   0.002   PHE A 330 
   TYR   0.020   0.001   TYR N  80 
   ARG   0.007   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 203
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 5
  residues processed: 206
  average time/residue: 0.2433
  time to fit residues: 66.0996
Evaluate side-chains
  210 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 205
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1456
  time to fit residues: 2.3526
-------------------------------------------------------------------------------
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:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8482  Z= 0.282
  Angle     :  0.635   7.660  11502  Z= 0.328
  Chirality :  0.045   0.179   1299
  Planarity :  0.005   0.053   1459
  Dihedral  :  5.749  59.350   1155
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 22.06 %
    Favored  : 77.72 %
  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: -1.35 (0.26), residues: 1030
  helix:  0.60 (0.28), residues: 385
  sheet: -1.71 (0.34), residues: 206
  loop : -1.79 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  82 
   HIS   0.004   0.001   HIS R 180 
   PHE   0.024   0.002   PHE R 282 
   TYR   0.019   0.002   TYR N  80 
   ARG   0.007   0.000   ARG A 332 

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 195
  time to evaluate  : 0.941 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 195
  average time/residue: 0.2421
  time to fit residues: 62.4774
Evaluate side-chains
  201 residues out of total 902 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0883
  time to fit residues: 1.5656
-------------------------------------------------------------------------------
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:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.157617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.142062 restraints weight = 11690.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 1.84
r_work: 0.3656 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8482  Z= 0.246
  Angle     :  0.618   7.104  11502  Z= 0.319
  Chirality :  0.044   0.168   1299
  Planarity :  0.004   0.053   1459
  Dihedral  :  5.662  58.819   1155
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 22.51 %
    Favored  : 77.16 %
  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: -1.32 (0.27), residues: 1030
  helix:  0.57 (0.28), residues: 387
  sheet: -1.70 (0.34), residues: 206
  loop : -1.72 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 271 
   HIS   0.003   0.001   HIS A 347 
   PHE   0.024   0.002   PHE R 282 
   TYR   0.019   0.002   TYR N  80 
   ARG   0.008   0.000   ARG B 304 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2302.47 seconds
wall clock time: 42 minutes 16.36 seconds (2536.36 seconds total)