Starting phenix.real_space_refine
on Fri Dec  8 04:47:44 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy7_33513/12_2023/7xy7_33513_updated.pdb"
  }
  resolution = 3.26
  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=   0.021
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      47      5.16       5
     C    4481      2.51       5
     N    1231      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE  328": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  341": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  364": "OD1" <-> "OD2"
    Residue "B ASP   66": "OD1" <-> "OD2"
    Residue "B ASP  118": "OD1" <-> "OD2"
    Residue "B ASP  153": "OD1" <-> "OD2"
    Residue "B ASP  212": "OD1" <-> "OD2"
    Residue "B PHE  234": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  290": "OD1" <-> "OD2"
    Residue "B ASP  298": "OD1" <-> "OD2"
    Residue "B ASP  303": "OD1" <-> "OD2"
    Residue "B ASP  323": "OD1" <-> "OD2"
    Residue "R PHE   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE   84": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  217": not complete - not flipped
    Residue "R TYR  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 7047
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1857
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 396
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
    Chain: "R"
      Number of atoms: 2211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2211
          Unusual residues: {'NEC': 1}
          Classifications: {'peptide': 283, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 271, None: 1}
            Not linked:
              pdbres="TYR R 308 "
              pdbres="NEC R 501 "
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 4.16, per 1000 atoms: 0.59
  Number of scatterers: 7047
  At special positions: 0
  Unit cell: (78.72, 101.76, 134.4, 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      47     16.00
     O    1288      8.00
     N    1231      7.00
     C    4481      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 171 " 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: 2.70
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      41.7% alpha, 17.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 31
    Processing helix  chain 'A' and resid 227 through 229
      No H-bonds generated for 'chain 'A' and resid 227 through 229'
    Processing helix  chain 'A' and resid 250 through 261
      removed outlier: 3.582A  pdb=" N   SER A 258 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 259 " --> pdb=" O   ASP A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 291 through 294
      No H-bonds generated for 'chain 'A' and resid 291 through 294'
    Processing helix  chain 'A' and resid 296 through 298
      No H-bonds generated for 'chain 'A' and resid 296 through 298'
    Processing helix  chain 'A' and resid 315 through 334
      removed outlier: 3.631A  pdb=" N   ARG A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLU A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER A 332 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 373
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 13 through 20
      removed outlier: 3.713A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 47
      removed outlier: 3.682A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA G  45 " --> pdb=" O   CYS G  41 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   LYS G  46 " --> pdb=" O   GLU G  42 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLU G  47 " --> pdb=" O   ALA G  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 6 through 34
      removed outlier: 4.140A  pdb=" N   LEU R  27 " --> pdb=" O   ALA R  23 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   VAL R  28 " --> pdb=" O   GLY R  24 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS R  29 " --> pdb=" O   ASN R  25 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 69
      removed outlier: 4.299A  pdb=" N   PHE R  45 " --> pdb=" O   PRO R  41 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU R  46 " --> pdb=" O   THR R  42 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   ILE R  61 " --> pdb=" O   GLY R  57 " (cutoff:3.500A)
      Proline residue:  R  62  - end of helix
    Processing helix  chain 'R' and resid 76 through 108
      removed outlier: 3.953A  pdb=" N   PHE R  80 " --> pdb=" O   TYR R  76 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   LEU R  81 " --> pdb=" O   GLY R  77 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   SER R  92 " --> pdb=" O   LEU R  88 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE R  93 " --> pdb=" O   THR R  89 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE R 107 " --> pdb=" O   ARG R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 116
      No H-bonds generated for 'chain 'R' and resid 113 through 116'
    Processing helix  chain 'R' and resid 119 through 142
      removed outlier: 3.683A  pdb=" N   THR R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
      Proline residue:  R 140  - end of helix
    Processing helix  chain 'R' and resid 173 through 176
      No H-bonds generated for 'chain 'R' and resid 173 through 176'
    Processing helix  chain 'R' and resid 179 through 182
      No H-bonds generated for 'chain 'R' and resid 179 through 182'
    Processing helix  chain 'R' and resid 192 through 217
      removed outlier: 3.641A  pdb=" N   PHE R 206 " --> pdb=" O   TYR R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 225 through 259
      removed outlier: 3.742A  pdb=" N   HIS R 231 " --> pdb=" O   GLN R 227 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   MET R 238 " --> pdb=" O   LYS R 234 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ILE R 239 " --> pdb=" O   SER R 235 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL R 240 " --> pdb=" O   LEU R 236 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE R 243 " --> pdb=" O   ILE R 239 " (cutoff:3.500A)
      Proline residue:  R 249  - end of helix
    Processing helix  chain 'R' and resid 261 through 265
    Processing helix  chain 'R' and resid 269 through 290
      removed outlier: 3.582A  pdb=" N   MET R 274 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN R 282 " --> pdb=" O   SER R 279 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   SER R 283 " --> pdb=" O   HIS R 280 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL R 284 " --> pdb=" O   ALA R 281 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   ASN R 286 " --> pdb=" O   SER R 283 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
      removed outlier: 3.594A  pdb=" N   TYR R 290 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 307
    Processing sheet with id=  A, first strand: chain 'A' and resid 269 through 275
      removed outlier: 4.204A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A  37 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   LEU A  36 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   HIS A 213 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   LEU A  38 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE A 215 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.886A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.749A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.121A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.600A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.441A  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: 6.926A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.598A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B 308 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 327 through 330
      removed outlier: 3.658A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    852 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: 1.88

  Time building geometry restraints manager: 2.87 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: 2296
        1.34 -     1.46: 1024
        1.46 -     1.57: 3805
        1.57 -     1.69: 0
        1.69 -     1.81: 65
  Bond restraints: 7190
  Sorted by residual:
  bond pdb=" C4  NEC R 501 "
       pdb=" C5  NEC R 501 "
    ideal  model  delta    sigma   weight residual
    1.385  1.471 -0.086 2.00e-02 2.50e+03 1.84e+01
  bond pdb=" C5  NEC R 501 "
       pdb=" C6  NEC R 501 "
    ideal  model  delta    sigma   weight residual
    1.407  1.482 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" C8  NEC R 501 "
       pdb=" N7  NEC R 501 "
    ideal  model  delta    sigma   weight residual
    1.302  1.357 -0.055 2.00e-02 2.50e+03 7.65e+00
  bond pdb=" C3' NEC R 501 "
       pdb=" O3' NEC R 501 "
    ideal  model  delta    sigma   weight residual
    1.393  1.433 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" C2' NEC R 501 "
       pdb=" O2' NEC R 501 "
    ideal  model  delta    sigma   weight residual
    1.400  1.434 -0.034 2.00e-02 2.50e+03 2.89e+00
  ... (remaining 7185 not shown)

  Histogram of bond angle deviations from ideal:
      100.03 -   107.26: 190
      107.26 -   114.49: 4228
      114.49 -   121.72: 3764
      121.72 -   128.95: 1515
      128.95 -   136.18: 55
  Bond angle restraints: 9752
  Sorted by residual:
  angle pdb=" C2  NEC R 501 "
        pdb=" N3  NEC R 501 "
        pdb=" C4  NEC R 501 "
      ideal   model   delta    sigma   weight residual
     111.54  120.89   -9.35 3.00e+00 1.11e-01 9.71e+00
  angle pdb=" CA  LEU B 198 "
        pdb=" CB  LEU B 198 "
        pdb=" CG  LEU B 198 "
      ideal   model   delta    sigma   weight residual
     116.30  126.02   -9.72 3.50e+00 8.16e-02 7.70e+00
  angle pdb=" C5  NEC R 501 "
        pdb=" C4  NEC R 501 "
        pdb=" N3  NEC R 501 "
      ideal   model   delta    sigma   weight residual
     126.75  118.68    8.07 3.00e+00 1.11e-01 7.23e+00
  angle pdb=" CA  GLN B  17 "
        pdb=" CB  GLN B  17 "
        pdb=" CG  GLN B  17 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.89e+00
  angle pdb=" CB  ARG A 339 "
        pdb=" CG  ARG A 339 "
        pdb=" CD  ARG A 339 "
      ideal   model   delta    sigma   weight residual
     111.30  117.23   -5.93 2.30e+00 1.89e-01 6.64e+00
  ... (remaining 9747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 4180
       35.44 -    70.87: 112
       70.87 -   106.31: 4
      106.31 -   141.74: 0
      141.74 -   177.18: 1
  Dihedral angle restraints: 4297
    sinusoidal: 1686
      harmonic: 2611
  Sorted by residual:
  dihedral pdb=" CB  CYS R  78 "
           pdb=" SG  CYS R  78 "
           pdb=" SG  CYS R 171 "
           pdb=" CB  CYS R 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.51  -69.51     1      1.00e+01 1.00e-02 6.24e+01
  dihedral pdb=" CB  GLU R 217 "
           pdb=" CG  GLU R 217 "
           pdb=" CD  GLU R 217 "
           pdb=" OE1 GLU R 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  177.18 -177.18     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  CYS R 171 "
           pdb=" C   CYS R 171 "
           pdb=" N   LEU R 172 "
           pdb=" CA  LEU R 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.32   18.68     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 4294 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 767
       0.037 -    0.074: 260
       0.074 -    0.111: 67
       0.111 -    0.149: 23
       0.149 -    0.186: 1
  Chirality restraints: 1118
  Sorted by residual:
  chirality pdb=" C2' NEC R 501 "
            pdb=" C1' NEC R 501 "
            pdb=" C3' NEC R 501 "
            pdb=" O2' NEC R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.54   -0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" CA  PRO R 249 "
            pdb=" N   PRO R 249 "
            pdb=" C   PRO R 249 "
            pdb=" CB  PRO R 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  ASP B 163 "
            pdb=" N   ASP B 163 "
            pdb=" C   ASP B 163 "
            pdb=" CB  ASP B 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 1115 not shown)

  Planarity restraints: 1239
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 193 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO R 194 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO R 194 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 194 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 314 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.83e+00
        pdb=" N   PRO A 315 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 118 "    0.006 2.00e-02 2.50e+03   1.26e-02 1.59e+00
        pdb=" CG  ASP B 118 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 118 "    0.008 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 118 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1236 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 142
        2.69 -     3.24: 6519
        3.24 -     3.80: 10502
        3.80 -     4.35: 13097
        4.35 -     4.90: 22292
  Nonbonded interactions: 52552
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.141 2.440
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.258 2.440
  nonbonded pdb=" OG1 THR B 173 "
            pdb=" OE1 GLN B 175 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OG  SER A   6 "
            pdb=" OE1 GLU A   8 "
     model   vdw
     2.260 2.440
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.276 2.440
  ... (remaining 52547 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          5.100
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     22.100
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
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   0.086   7190  Z= 0.215
  Angle     :  0.576   9.715   9752  Z= 0.307
  Chirality :  0.042   0.186   1118
  Planarity :  0.004   0.041   1239
  Dihedral  : 15.857 177.175   2600
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 17.72 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 881
  helix:  1.98 (0.28), residues: 369
  sheet:  0.61 (0.43), residues: 168
  loop : -0.72 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B  99 
   HIS   0.003   0.001   HIS B  54 
   PHE   0.020   0.001   PHE A 215 
   TYR   0.008   0.001   TYR R 104 
   ARG   0.007   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.820 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 171
  average time/residue: 0.2739
  time to fit residues: 57.7745
Evaluate side-chains
  166 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.767 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.4919
  time to fit residues: 1.5184
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.6758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.0633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7190  Z= 0.242
  Angle     :  0.493   7.569   9752  Z= 0.266
  Chirality :  0.042   0.129   1118
  Planarity :  0.004   0.045   1239
  Dihedral  :  4.187  24.994    999
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.48 %
    Favored  : 80.95 %
  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:  1.17 (0.29), residues: 881
  helix:  2.04 (0.28), residues: 376
  sheet:  0.68 (0.43), residues: 161
  loop : -0.58 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B 211 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.012   0.002   PHE B 199 
   TYR   0.010   0.001   TYR R 104 
   ARG   0.005   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 21
  residues processed: 176
  average time/residue: 0.3007
  time to fit residues: 64.2024
Evaluate side-chains
  191 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.765 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0919
  time to fit residues: 4.1856
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0970
   chunk 71 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7190  Z= 0.202
  Angle     :  0.467   8.542   9752  Z= 0.252
  Chirality :  0.041   0.129   1118
  Planarity :  0.003   0.045   1239
  Dihedral  :  3.928  17.795    999
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.80 %
    Favored  : 82.14 %
  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:  1.23 (0.29), residues: 881
  helix:  2.18 (0.28), residues: 376
  sheet:  0.68 (0.44), residues: 156
  loop : -0.65 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B 211 
   HIS   0.002   0.001   HIS G  44 
   PHE   0.012   0.001   PHE A 215 
   TYR   0.008   0.001   TYR A 322 
   ARG   0.005   0.000   ARG R 215 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 171
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 172
  average time/residue: 0.2972
  time to fit residues: 62.0629
Evaluate side-chains
  168 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 164
  time to evaluate  : 0.755 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1778
  time to fit residues: 2.0063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7190  Z= 0.252
  Angle     :  0.488   8.381   9752  Z= 0.263
  Chirality :  0.042   0.127   1118
  Planarity :  0.004   0.046   1239
  Dihedral  :  3.982  17.204    999
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.20 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.29), residues: 881
  helix:  2.10 (0.27), residues: 377
  sheet:  0.57 (0.43), residues: 161
  loop : -0.76 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  99 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.026   0.002   PHE A 215 
   TYR   0.009   0.001   TYR R  10 
   ARG   0.004   0.000   ARG B 256 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 23
  residues processed: 184
  average time/residue: 0.2850
  time to fit residues: 64.1001
Evaluate side-chains
  192 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.786 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0696
  time to fit residues: 4.0001
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7190  Z= 0.285
  Angle     :  0.517   8.727   9752  Z= 0.276
  Chirality :  0.043   0.131   1118
  Planarity :  0.004   0.046   1239
  Dihedral  :  4.212  23.610    999
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.12 %
    Favored  : 79.50 %
  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:  1.01 (0.29), residues: 881
  helix:  2.05 (0.27), residues: 377
  sheet:  0.49 (0.42), residues: 161
  loop : -0.81 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 211 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.020   0.002   PHE A 215 
   TYR   0.010   0.001   TYR R  10 
   ARG   0.003   0.000   ARG R 215 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 13
  residues processed: 184
  average time/residue: 0.2748
  time to fit residues: 61.9771
Evaluate side-chains
  189 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0678
  time to fit residues: 2.6585
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7190  Z= 0.273
  Angle     :  0.515   8.680   9752  Z= 0.275
  Chirality :  0.042   0.127   1118
  Planarity :  0.004   0.047   1239
  Dihedral  :  4.081  16.718    999
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.05 %
    Favored  : 79.10 %
  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:  1.01 (0.29), residues: 881
  helix:  2.08 (0.27), residues: 376
  sheet:  0.50 (0.43), residues: 161
  loop : -0.85 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  99 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.029   0.002   PHE A 215 
   TYR   0.009   0.001   TYR R  10 
   ARG   0.004   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 10
  residues processed: 181
  average time/residue: 0.2974
  time to fit residues: 65.5240
Evaluate side-chains
  187 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 0.779 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0722
  time to fit residues: 2.3890
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 48 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7190  Z= 0.228
  Angle     :  0.494   8.590   9752  Z= 0.265
  Chirality :  0.041   0.129   1118
  Planarity :  0.004   0.046   1239
  Dihedral  :  4.016  16.538    999
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.44 %
    Favored  : 78.70 %
  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:  1.05 (0.29), residues: 881
  helix:  2.13 (0.28), residues: 375
  sheet:  0.48 (0.42), residues: 161
  loop : -0.80 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  99 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.026   0.002   PHE A 215 
   TYR   0.008   0.001   TYR A 322 
   ARG   0.004   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 8
  residues processed: 179
  average time/residue: 0.2866
  time to fit residues: 63.5914
Evaluate side-chains
  175 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.749 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1294
  time to fit residues: 2.5759
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0470
   chunk 7 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 74 optimal weight:    0.0000
   overall best weight:    0.4282

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7190  Z= 0.179
  Angle     :  0.476   8.209   9752  Z= 0.254
  Chirality :  0.041   0.132   1118
  Planarity :  0.003   0.045   1239
  Dihedral  :  3.821  15.913    999
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 20.90 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.29), residues: 881
  helix:  2.23 (0.28), residues: 376
  sheet:  0.56 (0.43), residues: 161
  loop : -0.83 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  99 
   HIS   0.002   0.000   HIS G  44 
   PHE   0.022   0.001   PHE A 215 
   TYR   0.008   0.001   TYR R 104 
   ARG   0.004   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 158
  time to evaluate  : 0.792 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 161
  average time/residue: 0.2587
  time to fit residues: 52.2714
Evaluate side-chains
  163 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 159
  time to evaluate  : 0.750 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0814
  time to fit residues: 1.6396
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 83 optimal weight:    0.1980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7190  Z= 0.194
  Angle     :  0.490   8.723   9752  Z= 0.262
  Chirality :  0.041   0.150   1118
  Planarity :  0.003   0.046   1239
  Dihedral  :  3.869  21.551    999
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 22.09 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.29), residues: 881
  helix:  2.23 (0.28), residues: 376
  sheet:  0.68 (0.43), residues: 159
  loop : -0.87 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  99 
   HIS   0.002   0.000   HIS G  44 
   PHE   0.023   0.001   PHE A 215 
   TYR   0.009   0.001   TYR A 322 
   ARG   0.004   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.833 
Fit side-chains
  outliers start: 3
  outliers final: 3
  residues processed: 161
  average time/residue: 0.2577
  time to fit residues: 51.8900
Evaluate side-chains
  163 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.764 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0717
  time to fit residues: 1.4592
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0870
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7190  Z= 0.260
  Angle     :  0.519   8.885   9752  Z= 0.278
  Chirality :  0.042   0.142   1118
  Planarity :  0.004   0.046   1239
  Dihedral  :  3.978  18.531    999
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 22.35 %
    Favored  : 77.25 %
  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:  1.04 (0.29), residues: 881
  helix:  2.13 (0.28), residues: 375
  sheet:  0.60 (0.42), residues: 159
  loop : -0.90 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  99 
   HIS   0.003   0.001   HIS G  44 
   PHE   0.027   0.002   PHE A 215 
   TYR   0.010   0.001   TYR A 322 
   ARG   0.004   0.000   ARG B  49 

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

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

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1762 Ramachandran restraints generated.
    881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 171
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 171
  average time/residue: 0.2908
  time to fit residues: 60.7216
Evaluate side-chains
  172 residues out of total 759 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 170
  time to evaluate  : 0.763 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0787
  time to fit residues: 1.3394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0980
   chunk 29 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.131469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112537 restraints weight = 10481.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.42
r_work: 0.3317 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7190  Z= 0.217
  Angle     :  0.501   8.928   9752  Z= 0.268
  Chirality :  0.041   0.134   1118
  Planarity :  0.004   0.045   1239
  Dihedral  :  3.878  13.894    999
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 22.35 %
    Favored  : 77.12 %
  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:  1.08 (0.29), residues: 881
  helix:  2.19 (0.28), residues: 375
  sheet:  0.58 (0.42), residues: 159
  loop : -0.89 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  99 
   HIS   0.002   0.001   HIS G  44 
   PHE   0.024   0.001   PHE A 215 
   TYR   0.009   0.001   TYR A 322 
   ARG   0.004   0.000   ARG B  49 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2103.55 seconds
wall clock time: 38 minutes 23.48 seconds (2303.48 seconds total)