Starting phenix.real_space_refine
on Sun Dec 10 19:17:28 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cky_30394/12_2023/7cky_30394_neut_updated.pdb"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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 7222 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      53      5.16       5
     C    5171      2.51       5
     N    1408      2.21       5
     O    1494      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   13": "NH1" <-> "NH2"
    Residue "A GLU   15": "OE1" <-> "OE2"
    Residue "A GLU   21": "OE1" <-> "OE2"
    Residue "A ARG   42": "NH1" <-> "NH2"
    Residue "A GLU   50": "OE1" <-> "OE2"
    Residue "A GLU  299": "OE1" <-> "OE2"
    Residue "A GLU  314": "OE1" <-> "OE2"
    Residue "A GLU  327": "OE1" <-> "OE2"
    Residue "A GLU  370": "OE1" <-> "OE2"
    Residue "B GLU    3": "OE1" <-> "OE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B GLU   12": "OE1" <-> "OE2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B PHE  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   22": "OE1" <-> "OE2"
    Residue "G GLU   47": "OE1" <-> "OE2"
    Residue "N PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU   89": "OE1" <-> "OE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R GLU  132": "OE1" <-> "OE2"
    Residue "R ARG  227": "NH1" <-> "NH2"
  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: 8128
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1906
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2587
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2227
          Unusual residues: {'CLR': 1, 'G3U': 1}
          Classifications: {'peptide': 276, 'undetermined': 2}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 9, 'TRANS': 266, None: 2}
            Not linked:
              pdbres="LEU R 344 "
              pdbres="CLR R 501 "
            Not linked:
              pdbres="CLR R 501 "
              pdbres="G3U R 502 "
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
  Time building chain proxies: 4.88, per 1000 atoms: 0.60
  Number of scatterers: 8128
  At special positions: 0
  Unit cell: (90, 86, 123, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      53     16.00
     F       2      9.00
     O    1494      8.00
     N    1408      7.00
     C    5171      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, 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=1.96
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 186 " distance=1.44
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " 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: 3.14
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      38.5% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 39
      removed outlier: 3.729A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 58
    Processing helix  chain 'A' and resid 234 through 237
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 294 through 303
      removed outlier: 4.667A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 315
      No H-bonds generated for 'chain 'A' and resid 313 through 315'
    Processing helix  chain 'A' and resid 332 through 350
      removed outlier: 3.934A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
      removed outlier: 3.569A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 30 through 33
      removed outlier: 3.908A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 30 through 47
      removed outlier: 4.748A  pdb=" N   LYS G  46 " --> pdb=" O   GLU G  42 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLU G  47 " --> pdb=" O   ALA G  43 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'R' and resid 24 through 49
    Processing helix  chain 'R' and resid 58 through 76
      removed outlier: 3.967A  pdb=" N   PHE R  62 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU R  76 " --> pdb=" O   VAL R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 78 through 87
    Processing helix  chain 'R' and resid 93 through 126
      removed outlier: 4.714A  pdb=" N   ASN R  97 " --> pdb=" O   SER R  94 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   THR R 108 " --> pdb=" O   MET R 105 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER R 126 " --> pdb=" O   TRP R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 134
    Processing helix  chain 'R' and resid 137 through 160
      removed outlier: 4.576A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 192 through 202
      removed outlier: 3.835A  pdb=" N   ILE R 196 " --> pdb=" O   ARG R 192 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   SER R 197 " --> pdb=" O   THR R 193 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE R 201 " --> pdb=" O   SER R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 236
      removed outlier: 3.956A  pdb=" N   ALA R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 295
      removed outlier: 3.798A  pdb=" N   LYS R 269 " --> pdb=" O   LYS R 265 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL R 270 " --> pdb=" O   ARG R 266 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU R 271 " --> pdb=" O   GLU R 267 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   VAL R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 4.079A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 310 through 333
      removed outlier: 4.075A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER R 325 " --> pdb=" O   TRP R 321 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
      removed outlier: 4.381A  pdb=" N   PHE R 333 " --> pdb=" O   ILE R 329 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 343
      removed outlier: 3.822A  pdb=" N   ALA R 340 " --> pdb=" O   ASP R 336 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR R 343 " --> pdb=" O   LYS R 339 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 359 through 363
      removed outlier: 6.802A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.710A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 111 through 113
      removed outlier: 5.975A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 178 through 181
      removed outlier: 3.672A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.855A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.142A  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: 6.684A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.350A  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 317 through 320
      removed outlier: 3.738A  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 8
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.926A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    942 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: 2.23

  Time building geometry restraints manager: 3.41 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1308
        1.31 -     1.44: 2328
        1.44 -     1.56: 4591
        1.56 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 8299
  Sorted by residual:
  bond pdb=" C15 G3U R 502 "
       pdb=" C19 G3U R 502 "
    ideal  model  delta    sigma   weight residual
    1.484  1.386  0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" C24 G3U R 502 "
       pdb=" C26 G3U R 502 "
    ideal  model  delta    sigma   weight residual
    1.449  1.372  0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" C24 G3U R 502 "
       pdb=" N23 G3U R 502 "
    ideal  model  delta    sigma   weight residual
    1.379  1.316  0.063 2.00e-02 2.50e+03 9.85e+00
  bond pdb=" C10 G3U R 502 "
       pdb=" O11 G3U R 502 "
    ideal  model  delta    sigma   weight residual
    1.347  1.406 -0.059 2.00e-02 2.50e+03 8.56e+00
  bond pdb=" C19 G3U R 502 "
       pdb=" N20 G3U R 502 "
    ideal  model  delta    sigma   weight residual
    1.382  1.329  0.053 2.00e-02 2.50e+03 7.01e+00
  ... (remaining 8294 not shown)

  Histogram of bond angle deviations from ideal:
      100.20 -   106.97: 187
      106.97 -   113.73: 4602
      113.73 -   120.50: 3239
      120.50 -   127.26: 3147
      127.26 -   134.02: 88
  Bond angle restraints: 11263
  Sorted by residual:
  angle pdb=" C   TYR R 214 "
        pdb=" CA  TYR R 214 "
        pdb=" CB  TYR R 214 "
      ideal   model   delta    sigma   weight residual
     110.67  115.79   -5.12 1.92e+00 2.71e-01 7.12e+00
  angle pdb=" N   SER B 227 "
        pdb=" CA  SER B 227 "
        pdb=" C   SER B 227 "
      ideal   model   delta    sigma   weight residual
     108.34  111.69   -3.35 1.31e+00 5.83e-01 6.55e+00
  angle pdb=" CA  ASP B 186 "
        pdb=" C   ASP B 186 "
        pdb=" O   ASP B 186 "
      ideal   model   delta    sigma   weight residual
     120.92  118.22    2.70 1.14e+00 7.69e-01 5.62e+00
  angle pdb=" N   ASN R 292 "
        pdb=" CA  ASN R 292 "
        pdb=" C   ASN R 292 "
      ideal   model   delta    sigma   weight residual
     111.75  108.76    2.99 1.28e+00 6.10e-01 5.47e+00
  angle pdb=" C21 G3U R 502 "
        pdb=" N23 G3U R 502 "
        pdb=" C24 G3U R 502 "
      ideal   model   delta    sigma   weight residual
     127.77  121.01    6.76 3.00e+00 1.11e-01 5.08e+00
  ... (remaining 11258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 4401
       17.06 -    34.13: 462
       34.13 -    51.19: 77
       51.19 -    68.26: 24
       68.26 -    85.32: 10
  Dihedral angle restraints: 4974
    sinusoidal: 1949
      harmonic: 3025
  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
      93.00   60.49   32.51     1      1.00e+01 1.00e-02 1.50e+01
  dihedral pdb=" CA  ASP R  70 "
           pdb=" CB  ASP R  70 "
           pdb=" CG  ASP R  70 "
           pdb=" OD1 ASP R  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.03   56.03     1      2.00e+01 2.50e-03 1.06e+01
  dihedral pdb=" C   TYR R 214 "
           pdb=" N   TYR R 214 "
           pdb=" CA  TYR R 214 "
           pdb=" CB  TYR R 214 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.64    8.04     0      2.50e+00 1.60e-01 1.03e+01
  ... (remaining 4971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 976
       0.042 -    0.084: 236
       0.084 -    0.127: 66
       0.127 -    0.169: 2
       0.169 -    0.211: 1
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  TYR R 214 "
            pdb=" N   TYR R 214 "
            pdb=" C   TYR R 214 "
            pdb=" CB  TYR R 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  LEU R 190 "
            pdb=" N   LEU R 190 "
            pdb=" C   LEU R 190 "
            pdb=" CB  LEU R 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 205 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO R 206 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO R 206 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 206 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 327 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO R 328 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO R 328 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO R 328 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "   -0.016 5.00e-02 4.00e+02   2.43e-02 9.44e-01
        pdb=" N   PRO N  88 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1420 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 297
        2.70 -     3.25: 8480
        3.25 -     3.80: 14563
        3.80 -     4.35: 18720
        4.35 -     4.90: 30686
  Nonbonded interactions: 72746
  Sorted by model distance:
  nonbonded pdb=" O   PRO R 137 "
            pdb=" CD2 PHE R 141 "
     model   vdw
     2.154 3.340
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.186 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.239 2.440
  nonbonded pdb=" OG1 THR R 108 "
            pdb=" OG  SER R 202 "
     model   vdw
     2.262 2.440
  nonbonded pdb=" OG1 THR R  59 "
            pdb=" OD2 ASP R 120 "
     model   vdw
     2.282 2.440
  ... (remaining 72741 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:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.680
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     25.720
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4872
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.098   8299  Z= 0.189
  Angle     :  0.478   6.761  11263  Z= 0.285
  Chirality :  0.039   0.211   1281
  Planarity :  0.003   0.041   1423
  Dihedral  : 14.493  85.325   2996
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.24 %
    Favored  : 85.25 %
  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: -2.84 (0.24), residues: 1018
  helix: -0.77 (0.23), residues: 395
  sheet: -2.80 (0.33), residues: 192
  loop : -2.40 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 234 
   HIS   0.002   0.000   HIS B 311 
   PHE   0.006   0.001   PHE B 235 
   TYR   0.014   0.001   TYR R 214 
   ARG   0.003   0.000   ARG B 214 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 189
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 5
  residues processed: 200
  average time/residue: 0.2472
  time to fit residues: 63.8739
Evaluate side-chains
  152 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 147
  time to evaluate  : 0.897 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0808
  time to fit residues: 2.0060
-------------------------------------------------------------------------------
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:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0670
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
A 267 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
A 377 ASN
A 390 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  13 GLN
N  39 GLN
R  60 ASN
R 323 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5521
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8299  Z= 0.219
  Angle     :  0.578   9.311  11263  Z= 0.306
  Chirality :  0.042   0.159   1281
  Planarity :  0.005   0.037   1423
  Dihedral  :  4.672  44.202   1201
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.35 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.25), residues: 1018
  helix:  0.18 (0.25), residues: 399
  sheet: -2.52 (0.37), residues: 166
  loop : -2.05 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B 211 
   HIS   0.007   0.001   HIS A 357 
   PHE   0.028   0.002   PHE R 141 
   TYR   0.016   0.002   TYR N  94 
   ARG   0.008   0.001   ARG A 389 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 7
  residues processed: 179
  average time/residue: 0.2010
  time to fit residues: 49.2193
Evaluate side-chains
  150 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 143
  time to evaluate  : 0.962 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0801
  time to fit residues: 2.2007
-------------------------------------------------------------------------------
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:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.1980
   chunk 73 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  41 HIS
A 271 ASN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 125 ASN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8299  Z= 0.336
  Angle     :  0.659   8.145  11263  Z= 0.348
  Chirality :  0.044   0.217   1281
  Planarity :  0.005   0.063   1423
  Dihedral  :  4.923  53.558   1201
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 21.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.16 %
    Favored  : 77.47 %
  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: -1.75 (0.26), residues: 1018
  helix:  0.33 (0.26), residues: 394
  sheet: -2.49 (0.35), residues: 194
  loop : -1.86 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.003   TRP N  36 
   HIS   0.012   0.002   HIS A 357 
   PHE   0.040   0.002   PHE A 222 
   TYR   0.020   0.002   TYR B 264 
   ARG   0.014   0.001   ARG A 389 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 9
  residues processed: 203
  average time/residue: 0.2250
  time to fit residues: 60.4831
Evaluate side-chains
  174 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0790
  time to fit residues: 2.6688
-------------------------------------------------------------------------------
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:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 92 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 87 optimal weight:    0.4980
   chunk 26 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
R  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          0.5838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8299  Z= 0.217
  Angle     :  0.581   9.827  11263  Z= 0.298
  Chirality :  0.042   0.164   1281
  Planarity :  0.004   0.042   1423
  Dihedral  :  4.712  56.154   1201
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 19.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 19.40 %
    Favored  : 77.35 %
  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: -1.47 (0.26), residues: 1018
  helix:  0.51 (0.26), residues: 394
  sheet: -2.36 (0.34), residues: 196
  loop : -1.61 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP N  36 
   HIS   0.009   0.001   HIS A 357 
   PHE   0.017   0.001   PHE R 141 
   TYR   0.020   0.002   TYR N  94 
   ARG   0.008   0.000   ARG N 118 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 14
  residues processed: 191
  average time/residue: 0.2016
  time to fit residues: 52.7377
Evaluate side-chains
  178 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.008 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0821
  time to fit residues: 3.4728
-------------------------------------------------------------------------------
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:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0060
   chunk 40 optimal weight:    6.9990
   chunk 83 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0470
   chunk 0 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0670
   chunk 24 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.3834

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          0.6187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8299  Z= 0.186
  Angle     :  0.552   8.815  11263  Z= 0.281
  Chirality :  0.041   0.159   1281
  Planarity :  0.004   0.036   1423
  Dihedral  :  4.616  55.830   1201
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 23.81 %
    Favored  : 75.15 %
  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: 1018
  helix:  0.52 (0.26), residues: 394
  sheet: -2.21 (0.33), residues: 205
  loop : -1.47 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  99 
   HIS   0.009   0.001   HIS A 357 
   PHE   0.014   0.002   PHE R 156 
   TYR   0.018   0.001   TYR N  94 
   ARG   0.006   0.000   ARG A  38 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 175
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 3
  residues processed: 181
  average time/residue: 0.2045
  time to fit residues: 51.7822
Evaluate side-chains
  167 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 0.951 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0801
  time to fit residues: 1.7602
-------------------------------------------------------------------------------
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:    3.9990
   chunk 19 optimal weight:    0.0370
   chunk 57 optimal weight:   30.0000
   chunk 24 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0770
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.5216

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B  62 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8299  Z= 0.201
  Angle     :  0.551   8.129  11263  Z= 0.282
  Chirality :  0.041   0.156   1281
  Planarity :  0.004   0.035   1423
  Dihedral  :  4.493  54.998   1201
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 24.97 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.27), residues: 1018
  helix:  0.57 (0.26), residues: 395
  sheet: -2.13 (0.33), residues: 215
  loop : -1.28 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  99 
   HIS   0.007   0.001   HIS A 357 
   PHE   0.012   0.001   PHE R 141 
   TYR   0.011   0.001   TYR N  94 
   ARG   0.009   0.000   ARG N 118 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 12
  outliers final: 6
  residues processed: 179
  average time/residue: 0.1854
  time to fit residues: 46.5933
Evaluate side-chains
  167 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1264
  time to fit residues: 2.4119
-------------------------------------------------------------------------------
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:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   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  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.7425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8299  Z= 0.241
  Angle     :  0.589   7.970  11263  Z= 0.301
  Chirality :  0.042   0.148   1281
  Planarity :  0.004   0.043   1423
  Dihedral  :  4.617  54.402   1201
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 26.13 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.27), residues: 1018
  helix:  0.66 (0.26), residues: 389
  sheet: -1.97 (0.34), residues: 207
  loop : -1.19 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.002   TRP B 169 
   HIS   0.008   0.001   HIS A 357 
   PHE   0.011   0.001   PHE R 141 
   TYR   0.020   0.001   TYR G  40 
   ARG   0.009   0.000   ARG B 304 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 10
  residues processed: 189
  average time/residue: 0.2010
  time to fit residues: 51.9978
Evaluate side-chains
  174 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.866 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0789
  time to fit residues: 2.6595
-------------------------------------------------------------------------------
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:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0770
   chunk 9 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 88 optimal weight:    7.9990
   chunk 93 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6646
moved from start:          0.7863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8299  Z= 0.221
  Angle     :  0.585   7.908  11263  Z= 0.299
  Chirality :  0.042   0.151   1281
  Planarity :  0.004   0.052   1423
  Dihedral  :  4.642  54.841   1201
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 26.13 %
    Favored  : 73.29 %
  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: -0.91 (0.27), residues: 1018
  helix:  0.78 (0.27), residues: 389
  sheet: -1.85 (0.35), residues: 205
  loop : -1.15 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 281 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.010   0.001   PHE R 141 
   TYR   0.017   0.001   TYR G  40 
   ARG   0.011   0.000   ARG B 251 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 171
  average time/residue: 0.1999
  time to fit residues: 47.3389
Evaluate side-chains
  155 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.904 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0788
  time to fit residues: 1.5442
-------------------------------------------------------------------------------
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:    2.9990
   chunk 93 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.8176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8299  Z= 0.217
  Angle     :  0.575   8.046  11263  Z= 0.295
  Chirality :  0.042   0.146   1281
  Planarity :  0.004   0.031   1423
  Dihedral  :  4.604  54.999   1201
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 26.95 %
    Favored  : 72.47 %
  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: -0.78 (0.27), residues: 1018
  helix:  0.84 (0.27), residues: 388
  sheet: -1.70 (0.37), residues: 188
  loop : -1.13 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B  99 
   HIS   0.007   0.001   HIS A 357 
   PHE   0.011   0.001   PHE B 235 
   TYR   0.017   0.001   TYR G  40 
   ARG   0.005   0.000   ARG N  72 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 166
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 171
  average time/residue: 0.2083
  time to fit residues: 49.4059
Evaluate side-chains
  156 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0862
  time to fit residues: 1.9822
-------------------------------------------------------------------------------
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:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 61 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:    0.2980
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 ASN
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.8536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8299  Z= 0.207
  Angle     :  0.572   8.186  11263  Z= 0.295
  Chirality :  0.042   0.145   1281
  Planarity :  0.004   0.033   1423
  Dihedral  :  4.594  55.330   1201
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 26.95 %
    Favored  : 72.47 %
  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: -0.78 (0.27), residues: 1018
  helix:  0.84 (0.27), residues: 386
  sheet: -1.62 (0.35), residues: 203
  loop : -1.13 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B 169 
   HIS   0.007   0.001   HIS A 357 
   PHE   0.013   0.001   PHE B 253 
   TYR   0.016   0.001   TYR G  40 
   ARG   0.007   0.000   ARG B 251 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 168
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 1
  residues processed: 170
  average time/residue: 0.1943
  time to fit residues: 45.7758
Evaluate side-chains
  154 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.942 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1014
  time to fit residues: 1.4203
-------------------------------------------------------------------------------
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:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 57 optimal weight:   10.0000
   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  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B 125 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN
N   3 GLN
** R 164 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.214180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.176238 restraints weight = 8925.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 2.19
r_work: 0.3848 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.8988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8299  Z= 0.263
  Angle     :  0.619  15.268  11263  Z= 0.316
  Chirality :  0.043   0.158   1281
  Planarity :  0.004   0.041   1423
  Dihedral  :  4.690  53.339   1201
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 18.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 27.18 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.27), residues: 1018
  helix:  0.83 (0.27), residues: 386
  sheet: -1.73 (0.34), residues: 213
  loop : -0.98 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B 211 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.013   0.002   PHE B 253 
   TYR   0.017   0.002   TYR B 264 
   ARG   0.007   0.000   ARG B 251 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2098.28 seconds
wall clock time: 38 minutes 49.58 seconds (2329.58 seconds total)