Starting phenix.real_space_refine
on Tue Nov 14 07:15:53 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9l_31824/11_2023/7v9l_31824.pdb"
  }
  resolution = 2.6
  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=   0.022
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      45      5.16       5
     C    5108      2.51       5
     N    1404      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  228": "NH1" <-> "NH2"
    Residue "A GLU  230": "OE1" <-> "OE2"
    Residue "A GLU  309": "OE1" <-> "OE2"
    Residue "A ARG  380": "NH1" <-> "NH2"
    Residue "A GLU  392": "OE1" <-> "OE2"
    Residue "R ARG   92": "NH1" <-> "NH2"
    Residue "R ARG  175": "NH1" <-> "NH2"
    Residue "R GLU  248": "OE1" <-> "OE2"
    Residue "R ARG  293": "NH1" <-> "NH2"
    Residue "R GLU  297": "OE1" <-> "OE2"
    Residue "R GLU  318": "OE1" <-> "OE2"
    Residue "Y GLU   22": "OE1" <-> "OE2"
    Residue "N GLU   46": "OE1" <-> "OE2"
    Residue "N TYR   95": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B GLU   12": "OE1" <-> "OE2"
    Residue "B ARG  129": "NH1" <-> "NH2"
    Residue "B GLU  130": "OE1" <-> "OE2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 8047
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1964
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 6, 'TRANS': 230}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2064
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 2
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    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: "B"
      Number of atoms: 2613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2613
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 4.78, per 1000 atoms: 0.59
  Number of scatterers: 8047
  At special positions: 0
  Unit cell: (97.185, 96.14, 118.085, 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      45     16.00
     O    1490      8.00
     N    1404      7.00
     C    5108      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 138 " - pdb=" SG  CYS R 208 " distance=2.04

  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: 3.20
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1912

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.8% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 39
    Processing helix  chain 'A' and resid 52 through 64
    Processing helix  chain 'A' and resid 233 through 241
      removed outlier: 4.301A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
      removed outlier: 3.864A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.988A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.658A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 63 through 90
    Processing helix  chain 'R' and resid 91 through 94
    Processing helix  chain 'R' and resid 95 through 125
    Processing helix  chain 'R' and resid 134 through 169
      removed outlier: 3.679A  pdb=" N   CYS R 138 " --> pdb=" O   SER R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 201
      removed outlier: 3.566A  pdb=" N   PHE R 178 " --> pdb=" O   SER R 174 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TRP R 179 " --> pdb=" O   ARG R 175 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP R 180 " --> pdb=" O   ARG R 176 " (cutoff:3.500A)
      Proline residue:  R 189  - end of helix
    Processing helix  chain 'R' and resid 214 through 248
      removed outlier: 3.714A  pdb=" N   TRP R 219 " --> pdb=" O   SER R 215 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   ILE R 220 " --> pdb=" O   PRO R 216 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   ILE R 221 " --> pdb=" O   TYR R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
    Processing helix  chain 'R' and resid 257 through 275
      removed outlier: 3.677A  pdb=" N   TRP R 261 " --> pdb=" O   GLN R 257 " (cutoff:3.500A)
      Proline residue:  R 272  - end of helix
    Processing helix  chain 'R' and resid 276 through 282
      removed outlier: 3.516A  pdb=" N   ILE R 280 " --> pdb=" O   HIS R 277 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ASN R 282 " --> pdb=" O   ILE R 279 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 289 through 298
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 298 through 313
      removed outlier: 3.548A  pdb=" N   PHE R 303 " --> pdb=" O   GLY R 299 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLY R 305 " --> pdb=" O   GLY R 301 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   PHE R 306 " --> pdb=" O   SER R 302 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 327
    Processing helix  chain 'Y' and resid 7 through 24
    Processing helix  chain 'Y' and resid 29 through 45
    Processing helix  chain 'Y' and resid 46 through 48
      No H-bonds generated for 'chain 'Y' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.844A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.521A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.436A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.743A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.704A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.575A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.763A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234
      removed outlier: 6.435A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.314A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1176 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: 2.45

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2634
        1.34 -     1.46: 1884
        1.46 -     1.58: 3640
        1.58 -     1.70: 0
        1.70 -     1.82: 61
  Bond restraints: 8219
  Sorted by residual:
  bond pdb=" CG1 ILE B  43 "
       pdb=" CD1 ILE B  43 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.92e+00
  bond pdb=" C   SER R 134 "
       pdb=" N   THR R 135 "
    ideal  model  delta    sigma   weight residual
    1.335  1.319  0.016 1.38e-02 5.25e+03 1.39e+00
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.32e+00
  bond pdb=" CB  MET B  61 "
       pdb=" CG  MET B  61 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CG  ASP B 163 "
       pdb=" OD1 ASP B 163 "
    ideal  model  delta    sigma   weight residual
    1.249  1.229  0.020 1.90e-02 2.77e+03 1.07e+00
  ... (remaining 8214 not shown)

  Histogram of bond angle deviations from ideal:
       98.66 -   105.74: 123
      105.74 -   112.82: 4352
      112.82 -   119.89: 2736
      119.89 -   126.97: 3818
      126.97 -   134.04: 108
  Bond angle restraints: 11137
  Sorted by residual:
  angle pdb=" CA  TYR R  69 "
        pdb=" CB  TYR R  69 "
        pdb=" CG  TYR R  69 "
      ideal   model   delta    sigma   weight residual
     113.90  120.49   -6.59 1.80e+00 3.09e-01 1.34e+01
  angle pdb=" CB  MET B  61 "
        pdb=" CG  MET B  61 "
        pdb=" SD  MET B  61 "
      ideal   model   delta    sigma   weight residual
     112.70  103.94    8.76 3.00e+00 1.11e-01 8.52e+00
  angle pdb=" C   PHE A 238 "
        pdb=" N   ASN A 239 "
        pdb=" CA  ASN A 239 "
      ideal   model   delta    sigma   weight residual
     120.38  124.51   -4.13 1.46e+00 4.69e-01 8.00e+00
  angle pdb=" CA  TRP A 234 "
        pdb=" CB  TRP A 234 "
        pdb=" CG  TRP A 234 "
      ideal   model   delta    sigma   weight residual
     113.60  118.80   -5.20 1.90e+00 2.77e-01 7.48e+00
  angle pdb=" CA  TRP R 155 "
        pdb=" CB  TRP R 155 "
        pdb=" CG  TRP R 155 "
      ideal   model   delta    sigma   weight residual
     113.60  108.41    5.19 1.90e+00 2.77e-01 7.46e+00
  ... (remaining 11132 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4487
       17.89 -    35.78: 315
       35.78 -    53.67: 42
       53.67 -    71.55: 9
       71.55 -    89.44: 9
  Dihedral angle restraints: 4862
    sinusoidal: 1907
      harmonic: 2955
  Sorted by residual:
  dihedral pdb=" CA  TYR A 253 "
           pdb=" C   TYR A 253 "
           pdb=" N   ARG A 265 "
           pdb=" CA  ARG A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.04   27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  ASP B 163 "
           pdb=" C   ASP B 163 "
           pdb=" N   THR B 164 "
           pdb=" CA  THR B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.04  -27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  MET B  61 "
           pdb=" C   MET B  61 "
           pdb=" N   HIS B  62 "
           pdb=" CA  HIS B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.38   27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 4859 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 773
       0.039 -    0.078: 342
       0.078 -    0.116: 113
       0.116 -    0.155: 19
       0.155 -    0.194: 5
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  TRP R 155 "
            pdb=" N   TRP R 155 "
            pdb=" C   TRP R 155 "
            pdb=" CB  TRP R 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.41e-01
  chirality pdb=" CA  THR A 284 "
            pdb=" N   THR A 284 "
            pdb=" C   THR A 284 "
            pdb=" CB  THR A 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CB  THR A 210 "
            pdb=" CA  THR A 210 "
            pdb=" OG1 THR A 210 "
            pdb=" CG2 THR A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1249 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 314 "   -0.125 9.50e-02 1.11e+02   7.28e-02 2.87e+01
        pdb=" NE  ARG B 314 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 314 "   -0.088 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 314 "    0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 314 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 342 "    0.089 9.50e-02 1.11e+02   5.29e-02 1.61e+01
        pdb=" NE  ARG A 342 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 342 "    0.066 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 342 "   -0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 342 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  49 "   -0.084 9.50e-02 1.11e+02   4.87e-02 1.29e+01
        pdb=" NE  ARG B  49 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  49 "   -0.059 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  49 "    0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  49 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 137
        2.68 -     3.23: 8196
        3.23 -     3.79: 13368
        3.79 -     4.34: 18670
        4.34 -     4.90: 30293
  Nonbonded interactions: 70664
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 228 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.120 2.520
  nonbonded pdb=" OH  TYR N 117 "
            pdb=" OD1 ASP B 228 "
     model   vdw
     2.191 2.440
  nonbonded pdb=" NH1 ARG B  22 "
            pdb=" O   ASP B 258 "
     model   vdw
     2.276 2.520
  nonbonded pdb=" O   PHE R 269 "
            pdb=" OH  TYR R 312 "
     model   vdw
     2.295 2.440
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.295 2.440
  ... (remaining 70659 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:             0.470
  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:          2.700
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.560
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
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   0.054   8219  Z= 0.284
  Angle     :  0.691   8.757  11137  Z= 0.409
  Chirality :  0.047   0.194   1252
  Planarity :  0.007   0.073   1416
  Dihedral  : 13.080  89.442   2947
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  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:  0.00 (0.26), residues: 1003
  helix:  0.49 (0.24), residues: 359
  sheet:  0.03 (0.35), residues: 207
  loop : -0.27 (0.31), residues: 437

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 1
  residues processed: 202
  average time/residue: 1.2096
  time to fit residues: 258.7069
Evaluate side-chains
  175 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 174
  time to evaluate  : 0.855 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1304
  time to fit residues: 1.5831
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
A 271 ASN
B 125 ASN
B 155 ASN
B 230 ASN
B 239 ASN
B 268 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6607
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8219  Z= 0.267
  Angle     :  0.587   5.835  11137  Z= 0.318
  Chirality :  0.043   0.151   1252
  Planarity :  0.004   0.042   1416
  Dihedral  :  5.377  25.580   1107
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.56 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1003
  helix:  1.74 (0.25), residues: 367
  sheet:  0.09 (0.33), residues: 203
  loop :  0.04 (0.32), residues: 433

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 9
  residues processed: 187
  average time/residue: 1.2093
  time to fit residues: 239.5519
Evaluate side-chains
  182 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 3
  residues processed: 6
  average time/residue: 0.3323
  time to fit residues: 3.5960
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0470
   chunk 97 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8219  Z= 0.237
  Angle     :  0.537   5.456  11137  Z= 0.291
  Chirality :  0.042   0.147   1252
  Planarity :  0.004   0.042   1416
  Dihedral  :  4.921  24.464   1107
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.71 %
    Favored  : 85.53 %
  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: 1003
  helix:  2.15 (0.26), residues: 365
  sheet: -0.09 (0.33), residues: 203
  loop :  0.01 (0.32), residues: 435

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 11
  residues processed: 197
  average time/residue: 1.1796
  time to fit residues: 246.4156
Evaluate side-chains
  189 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.861 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 5
  residues processed: 6
  average time/residue: 0.1242
  time to fit residues: 2.3443
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8219  Z= 0.302
  Angle     :  0.558   7.232  11137  Z= 0.299
  Chirality :  0.043   0.159   1252
  Planarity :  0.004   0.045   1416
  Dihedral  :  4.891  26.482   1107
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.89 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1003
  helix:  2.09 (0.26), residues: 368
  sheet: -0.19 (0.33), residues: 203
  loop : -0.16 (0.31), residues: 432

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 15
  residues processed: 190
  average time/residue: 1.2887
  time to fit residues: 259.5420
Evaluate side-chains
  191 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.948 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 7
  residues processed: 8
  average time/residue: 0.1339
  time to fit residues: 2.9377
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:   30.0000
   chunk 85 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6620
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8219  Z= 0.286
  Angle     :  0.548   6.765  11137  Z= 0.294
  Chirality :  0.043   0.159   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.777  25.958   1107
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.35 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1003
  helix:  2.05 (0.26), residues: 370
  sheet: -0.39 (0.32), residues: 211
  loop : -0.25 (0.32), residues: 422

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 14
  residues processed: 188
  average time/residue: 1.2189
  time to fit residues: 242.8080
Evaluate side-chains
  187 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.879 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 8
  residues processed: 6
  average time/residue: 0.4638
  time to fit residues: 4.4975
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
R  98 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8219  Z= 0.236
  Angle     :  0.528   5.964  11137  Z= 0.283
  Chirality :  0.042   0.154   1252
  Planarity :  0.004   0.046   1416
  Dihedral  :  4.622  23.983   1107
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.61 %
    Favored  : 81.86 %
  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:  0.88 (0.27), residues: 1003
  helix:  2.31 (0.26), residues: 363
  sheet: -0.57 (0.32), residues: 214
  loop : -0.24 (0.32), residues: 426

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 12
  residues processed: 191
  average time/residue: 1.2296
  time to fit residues: 248.6244
Evaluate side-chains
  189 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 0.967 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 9
  residues processed: 3
  average time/residue: 0.1154
  time to fit residues: 1.8793
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0980
   chunk 80 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 44 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
R  98 ASN
N  31 ASN
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8219  Z= 0.251
  Angle     :  0.536  10.055  11137  Z= 0.284
  Chirality :  0.042   0.143   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.608  23.861   1107
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.38 %
    Favored  : 82.09 %
  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:  0.85 (0.27), residues: 1003
  helix:  2.32 (0.26), residues: 363
  sheet: -0.60 (0.32), residues: 214
  loop : -0.29 (0.32), residues: 426

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 13
  residues processed: 202
  average time/residue: 1.1716
  time to fit residues: 251.1589
Evaluate side-chains
  198 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 185
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 9
  residues processed: 4
  average time/residue: 0.6592
  time to fit residues: 4.2294
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
R  98 ASN
N  31 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6611
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8219  Z= 0.243
  Angle     :  0.532   5.888  11137  Z= 0.283
  Chirality :  0.042   0.174   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.577  23.021   1107
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.45 %
    Favored  : 80.14 %
  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:  0.84 (0.27), residues: 1003
  helix:  2.36 (0.26), residues: 363
  sheet: -0.64 (0.32), residues: 214
  loop : -0.32 (0.32), residues: 426

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 14
  residues processed: 199
  average time/residue: 1.2091
  time to fit residues: 254.9899
Evaluate side-chains
  198 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.884 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 10
  residues processed: 4
  average time/residue: 0.1557
  time to fit residues: 2.1921
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    0.3980
   chunk 27 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
B 239 ASN
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8219  Z= 0.246
  Angle     :  0.536   8.992  11137  Z= 0.284
  Chirality :  0.042   0.152   1252
  Planarity :  0.004   0.047   1416
  Dihedral  :  4.557  22.073   1107
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.57 %
    Favored  : 80.25 %
  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:  0.82 (0.27), residues: 1003
  helix:  2.34 (0.26), residues: 364
  sheet: -0.63 (0.33), residues: 203
  loop : -0.37 (0.31), residues: 436

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 14
  residues processed: 193
  average time/residue: 1.2824
  time to fit residues: 261.7585
Evaluate side-chains
  196 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 1.034 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 10
  residues processed: 4
  average time/residue: 0.7043
  time to fit residues: 4.4949
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:   20.0000
   chunk 62 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
R  98 ASN
R 130 HIS
** Y  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8219  Z= 0.286
  Angle     :  0.542   5.751  11137  Z= 0.290
  Chirality :  0.043   0.169   1252
  Planarity :  0.004   0.049   1416
  Dihedral  :  4.635  21.993   1107
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.03 %
    Favored  : 80.48 %
  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:  0.70 (0.27), residues: 1003
  helix:  2.18 (0.26), residues: 370
  sheet: -0.72 (0.32), residues: 214
  loop : -0.38 (0.32), residues: 419

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

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

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2006 Ramachandran restraints generated.
    1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 13
  residues processed: 193
  average time/residue: 1.2221
  time to fit residues: 250.2863
Evaluate side-chains
  196 residues out of total 872 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 0.959 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 9
  residues processed: 4
  average time/residue: 0.1449
  time to fit residues: 2.1499
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0570
   chunk 14 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
R  98 ASN
B 239 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.152038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.133032 restraints weight = 10370.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 1.79
r_work: 0.3646 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8219  Z= 0.235
  Angle     :  0.536   9.384  11137  Z= 0.283
  Chirality :  0.042   0.154   1252
  Planarity :  0.004   0.049   1416
  Dihedral  :  4.547  21.282   1107
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.80 %
    Favored  : 80.37 %
  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:  0.73 (0.27), residues: 1003
  helix:  2.24 (0.26), residues: 370
  sheet: -0.76 (0.32), residues: 216
  loop : -0.35 (0.32), residues: 417
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4236.45 seconds
wall clock time: 75 minutes 44.24 seconds (4544.24 seconds total)