Starting phenix.real_space_refine
on Fri Dec  8 12:08:50 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wq4_32699/12_2023/7wq4_32699_updated.pdb"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      53      5.16       5
     C    5277      2.51       5
     N    1451      2.21       5
     O    1509      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R ARG  184": "NH1" <-> "NH2"
    Residue "B PHE  253": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8290
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2225
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 12, 'TRANS': 269}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 95
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
    Chain: "A"
      Number of atoms: 1927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1927
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "G"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 414
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.77, per 1000 atoms: 0.58
  Number of scatterers: 8290
  At special positions: 0
  Unit cell: (88.218, 97.344, 123.708, 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      53     16.00
     O    1509      8.00
     N    1451      7.00
     C    5277      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.22
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      37.7% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'R' and resid 27 through 51
      removed outlier: 3.611A  pdb=" N   VAL R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 87
      Proline residue:  R  80  - end of helix
    Processing helix  chain 'R' and resid 96 through 99
      No H-bonds generated for 'chain 'R' and resid 96 through 99'
    Processing helix  chain 'R' and resid 101 through 128
      removed outlier: 3.720A  pdb=" N   PHE R 106 " --> pdb=" O   HIS R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 163
      Proline residue:  R 159  - end of helix
      removed outlier: 4.804A  pdb=" N   SER R 162 " --> pdb=" O   GLY R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 195
    Processing helix  chain 'R' and resid 197 through 214
    Processing helix  chain 'R' and resid 225 through 248
    Processing helix  chain 'R' and resid 250 through 261
    Processing helix  chain 'R' and resid 268 through 292
      removed outlier: 3.696A  pdb=" N   ASN R 284 " --> pdb=" O   VAL R 280 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   SER R 285 " --> pdb=" O   SER R 281 " (cutoff:3.500A)
      Proline residue:  R 289  - end of helix
    Processing helix  chain 'R' and resid 297 through 306
      removed outlier: 3.760A  pdb=" N   LYS R 301 " --> pdb=" O   LYS R 297 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   GLY R 302 " --> pdb=" O   HIS R 298 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   PHE R 303 " --> pdb=" O   PHE R 299 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ARG R 304 " --> pdb=" O   ARG R 300 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   THR R 305 " --> pdb=" O   LYS R 301 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE R 306 " --> pdb=" O   GLY R 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 297 through 306'
    Processing helix  chain 'L' and resid 4 through 11
      removed outlier: 3.554A  pdb=" N   GLY L   8 " --> pdb=" O   LEU L   4 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TYR L   9 " --> pdb=" O   ASN L   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 30
      removed outlier: 3.583A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 55
      removed outlier: 4.407A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 115 through 129
      removed outlier: 4.077A  pdb=" N   GLN A 119 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   SER A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 184 through 202
      removed outlier: 3.549A  pdb=" N   PHE A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 242
      removed outlier: 4.292A  pdb=" N   ILE A 227 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.602A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    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 'G' and resid 12 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 56 through 58
      No H-bonds generated for 'chain 'G' and resid 56 through 58'
    Processing sheet with id=  A, first strand: chain 'R' and resid 165 through 169
    Processing sheet with id=  B, first strand: chain 'A' and resid 211 through 215
      removed outlier: 7.195A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   HIS A 214 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ASN A  80 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   LEU A  36 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   HIS A  82 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   LEU A  38 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.442A  pdb=" N   GLY A  40 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   VAL A  86 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.688A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.993A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.939A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.110A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 229 through 234
      removed outlier: 7.068A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.608A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.508A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.764A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)

    384 hydrogen bonds defined for protein.
    1050 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: 2.15

  Time building geometry restraints manager: 3.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2702
        1.34 -     1.46: 1972
        1.46 -     1.58: 3709
        1.58 -     1.70: 10
        1.70 -     1.81: 74
  Bond restraints: 8467
  Sorted by residual:
  bond pdb=" C5  CLR R 402 "
       pdb=" C6  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.332  1.651 -0.319 2.00e-02 2.50e+03 2.54e+02
  bond pdb=" C5  CLR R 401 "
       pdb=" C6  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.650 -0.318 2.00e-02 2.50e+03 2.53e+02
  bond pdb=" C15 CLR R 402 "
       pdb=" C16 CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.541  1.708 -0.167 2.00e-02 2.50e+03 6.99e+01
  bond pdb=" C15 CLR R 401 "
       pdb=" C16 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.541  1.705 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" C8  CLR R 402 "
       pdb=" C9  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.535  1.671 -0.136 2.00e-02 2.50e+03 4.62e+01
  ... (remaining 8462 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   107.22: 234
      107.22 -   113.91: 4782
      113.91 -   120.60: 3392
      120.60 -   127.28: 2988
      127.28 -   133.97: 93
  Bond angle restraints: 11489
  Sorted by residual:
  angle pdb=" N   VAL R 295 "
        pdb=" CA  VAL R 295 "
        pdb=" C   VAL R 295 "
      ideal   model   delta    sigma   weight residual
     113.71  106.66    7.05 9.50e-01 1.11e+00 5.51e+01
  angle pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
        pdb=" C7  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     125.11  111.58   13.53 3.00e+00 1.11e-01 2.04e+01
  angle pdb=" C5  CLR R 402 "
        pdb=" C6  CLR R 402 "
        pdb=" C7  CLR R 402 "
      ideal   model   delta    sigma   weight residual
     125.11  111.81   13.30 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" CA  ALA R 170 "
        pdb=" C   ALA R 170 "
        pdb=" O   ALA R 170 "
      ideal   model   delta    sigma   weight residual
     122.03  117.50    4.53 1.17e+00 7.31e-01 1.50e+01
  angle pdb=" C10 CLR R 401 "
        pdb=" C5  CLR R 401 "
        pdb=" C6  CLR R 401 "
      ideal   model   delta    sigma   weight residual
     122.94  111.81   11.13 3.00e+00 1.11e-01 1.38e+01
  ... (remaining 11484 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.16: 4849
       12.16 -    24.32: 191
       24.32 -    36.47: 60
       36.47 -    48.63: 26
       48.63 -    60.79: 9
  Dihedral angle restraints: 5135
    sinusoidal: 2094
      harmonic: 3041
  Sorted by residual:
  dihedral pdb=" N   PHE B 234 "
           pdb=" CA  PHE B 234 "
           pdb=" CB  PHE B 234 "
           pdb=" CG  PHE B 234 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.16  -59.84     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ARG R 184 "
           pdb=" CA  ARG R 184 "
           pdb=" CB  ARG R 184 "
           pdb=" CG  ARG R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.77   57.77     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CG  ARG R 184 "
           pdb=" CD  ARG R 184 "
           pdb=" NE  ARG R 184 "
           pdb=" CZ  ARG R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  139.10   40.90     2      1.50e+01 4.44e-03 9.14e+00
  ... (remaining 5132 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1271
       0.110 -    0.221: 27
       0.221 -    0.331: 4
       0.331 -    0.442: 2
       0.442 -    0.552: 2
  Chirality restraints: 1306
  Sorted by residual:
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.38   -0.55 2.00e-01 2.50e+01 7.62e+00
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.39   -0.54 2.00e-01 2.50e+01 7.33e+00
  chirality pdb=" C9  CLR R 402 "
            pdb=" C10 CLR R 402 "
            pdb=" C11 CLR R 402 "
            pdb=" C8  CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.86    0.42 2.00e-01 2.50e+01 4.35e+00
  ... (remaining 1303 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 101 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.52e+00
        pdb=" C   VAL R 101 "    0.021 2.00e-02 2.50e+03
        pdb=" O   VAL R 101 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   HIS R 102 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO B 236 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 158 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.12e+00
        pdb=" N   PRO R 159 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO R 159 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO R 159 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 2
        2.10 -     2.80: 2098
        2.80 -     3.50: 11036
        3.50 -     4.20: 19341
        4.20 -     4.90: 34428
  Nonbonded interactions: 66905
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN N  35 "
            pdb=" CB  ASP N  50 "
     model   vdw
     1.399 3.440
  nonbonded pdb=" CG2 VAL R 174 "
            pdb=" NE2 HIS R 176 "
     model   vdw
     2.067 3.540
  nonbonded pdb=" O   TYR R 129 "
            pdb=" OG  SER R 133 "
     model   vdw
     2.247 2.440
  nonbonded pdb=" O   THR R 191 "
            pdb=" OG  SER R 195 "
     model   vdw
     2.250 2.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.289 2.440
  ... (remaining 66900 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:             0.800
  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:          3.040
  Check model and map are aligned:         0.270
  Set scattering table:                    0.210
  Process input model:                     26.410
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
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      :  0.007   0.319   8467  Z= 0.511
  Angle     :  0.615  13.533  11489  Z= 0.339
  Chirality :  0.052   0.552   1306
  Planarity :  0.003   0.027   1450
  Dihedral  :  8.519  60.788   3162
  Min Nonbonded Distance : 1.399

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  3.38 %
    Favored  : 96.17 %
  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: -1.07 (0.24), residues: 1032
  helix:  0.15 (0.26), residues: 373
  sheet: -0.58 (0.31), residues: 237
  loop : -1.48 (0.27), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  82 
   HIS   0.002   0.000   HIS A 209 
   PHE   0.010   0.001   PHE R 103 
   TYR   0.005   0.001   TYR N  60 
   ARG   0.001   0.000   ARG N  72 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 251
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 255
  average time/residue: 1.2071
  time to fit residues: 325.8537
Evaluate side-chains
  165 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.955 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3069
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.0040
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
R  55 GLN
R  82 GLN
A  52 GLN
A  82 HIS
A 119 GLN
A 223 ASN
A 244 ASN
B  35 ASN
B 156 GLN
B 176 GLN
B 220 GLN
B 259 GLN
N  77 ASN
G  11 GLN
G  24 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8467  Z= 0.152
  Angle     :  0.490   7.414  11489  Z= 0.250
  Chirality :  0.040   0.151   1306
  Planarity :  0.003   0.027   1450
  Dihedral  :  4.475  50.333   1280
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.30 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1032
  helix:  1.32 (0.27), residues: 389
  sheet: -0.14 (0.32), residues: 229
  loop : -0.96 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP B 332 
   HIS   0.007   0.001   HIS A 209 
   PHE   0.016   0.002   PHE B 199 
   TYR   0.010   0.001   TYR G  40 
   ARG   0.005   0.000   ARG A 208 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 173
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 14
  residues processed: 189
  average time/residue: 1.1656
  time to fit residues: 234.4545
Evaluate side-chains
  159 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 0.960 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 6
  residues processed: 8
  average time/residue: 0.4215
  time to fit residues: 5.1906
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9980
   chunk 82 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
R  82 GLN
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 253 HIS
A 223 ASN
B  35 ASN
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
N  35 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8467  Z= 0.281
  Angle     :  0.583   6.992  11489  Z= 0.306
  Chirality :  0.044   0.177   1306
  Planarity :  0.004   0.034   1450
  Dihedral  :  4.982  54.884   1280
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 15.99 %
    Favored  : 79.28 %
  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:  0.22 (0.26), residues: 1032
  helix:  1.13 (0.27), residues: 395
  sheet:  0.10 (0.32), residues: 228
  loop : -0.71 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B 332 
   HIS   0.012   0.002   HIS A 209 
   PHE   0.015   0.002   PHE B 151 
   TYR   0.011   0.002   TYR R  86 
   ARG   0.006   0.001   ARG N 118 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 19
  residues processed: 161
  average time/residue: 1.2267
  time to fit residues: 210.0650
Evaluate side-chains
  141 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.995 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 15
  residues processed: 4
  average time/residue: 0.7709
  time to fit residues: 4.6760
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
A  52 GLN
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8467  Z= 0.194
  Angle     :  0.505   7.367  11489  Z= 0.265
  Chirality :  0.042   0.134   1306
  Planarity :  0.004   0.027   1450
  Dihedral  :  4.641  56.851   1280
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.47 %
    Favored  : 76.80 %
  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:  0.56 (0.26), residues: 1032
  helix:  1.39 (0.27), residues: 396
  sheet:  0.31 (0.33), residues: 223
  loop : -0.53 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.008   0.001   HIS A 209 
   PHE   0.014   0.002   PHE B 234 
   TYR   0.013   0.001   TYR B 124 
   ARG   0.006   0.000   ARG B 134 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 1.051 
Fit side-chains
  outliers start: 42
  outliers final: 26
  residues processed: 159
  average time/residue: 1.2989
  time to fit residues: 219.1047
Evaluate side-chains
  147 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 22
  residues processed: 4
  average time/residue: 0.9371
  time to fit residues: 5.3410
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 40 optimal weight:    0.1980
   chunk 84 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
B  35 ASN
** 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: 0.7234
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8467  Z= 0.213
  Angle     :  0.513   6.253  11489  Z= 0.271
  Chirality :  0.042   0.152   1306
  Planarity :  0.004   0.036   1450
  Dihedral  :  4.776  59.403   1280
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 19.37 %
    Favored  : 75.90 %
  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:  0.61 (0.26), residues: 1032
  helix:  1.40 (0.27), residues: 396
  sheet:  0.41 (0.33), residues: 227
  loop : -0.51 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.008   0.001   HIS A 209 
   PHE   0.014   0.002   PHE B 234 
   TYR   0.011   0.001   TYR A 243 
   ARG   0.007   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
  outliers start: 42
  outliers final: 25
  residues processed: 160
  average time/residue: 1.3329
  time to fit residues: 225.7903
Evaluate side-chains
  145 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 1.010 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 21
  residues processed: 4
  average time/residue: 0.7946
  time to fit residues: 4.7654
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0770
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
R  82 GLN
R 102 HIS
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
B  35 ASN
B  91 HIS
B 220 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.4657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8467  Z= 0.148
  Angle     :  0.471   7.800  11489  Z= 0.249
  Chirality :  0.040   0.135   1306
  Planarity :  0.003   0.038   1450
  Dihedral  :  4.536  58.668   1280
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.26 %
    Favored  : 76.35 %
  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:  0.83 (0.26), residues: 1032
  helix:  1.61 (0.27), residues: 396
  sheet:  0.50 (0.33), residues: 232
  loop : -0.41 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 209 
   PHE   0.012   0.001   PHE B 234 
   TYR   0.008   0.001   TYR A 243 
   ARG   0.009   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 137
  time to evaluate  : 1.047 
Fit side-chains
  outliers start: 39
  outliers final: 27
  residues processed: 168
  average time/residue: 1.2731
  time to fit residues: 227.0125
Evaluate side-chains
  154 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.946 
Switching outliers to nearest non-outliers
  outliers start: 27
  outliers final: 25
  residues processed: 2
  average time/residue: 0.0748
  time to fit residues: 1.5692
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 55 optimal weight:    0.0000
   chunk 83 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.9188

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
B  32 GLN
B  35 ASN
B 340 ASN
G  59 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8467  Z= 0.162
  Angle     :  0.484   7.163  11489  Z= 0.255
  Chirality :  0.041   0.133   1306
  Planarity :  0.003   0.031   1450
  Dihedral  :  4.519  56.528   1280
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.05 %
    Favored  : 75.34 %
  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:  0.89 (0.26), residues: 1032
  helix:  1.64 (0.27), residues: 395
  sheet:  0.58 (0.33), residues: 232
  loop : -0.39 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 209 
   PHE   0.011   0.001   PHE A  74 
   TYR   0.014   0.001   TYR R 129 
   ARG   0.007   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 41
  outliers final: 29
  residues processed: 165
  average time/residue: 1.2340
  time to fit residues: 216.1352
Evaluate side-chains
  160 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.991 
Switching outliers to nearest non-outliers
  outliers start: 29
  outliers final: 26
  residues processed: 3
  average time/residue: 0.5975
  time to fit residues: 3.3216
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0000
   overall best weight:    0.8988

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
A  24 GLN
B  32 GLN
B  35 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8467  Z= 0.163
  Angle     :  0.492   9.199  11489  Z= 0.258
  Chirality :  0.041   0.133   1306
  Planarity :  0.003   0.030   1450
  Dihedral  :  4.496  54.012   1280
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 20.27 %
    Favored  : 75.45 %
  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:  0.92 (0.26), residues: 1032
  helix:  1.68 (0.27), residues: 394
  sheet:  0.60 (0.33), residues: 232
  loop : -0.39 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 209 
   PHE   0.011   0.001   PHE A  74 
   TYR   0.015   0.001   TYR R 129 
   ARG   0.007   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 1.004 
Fit side-chains
  outliers start: 38
  outliers final: 28
  residues processed: 160
  average time/residue: 1.3151
  time to fit residues: 223.1544
Evaluate side-chains
  155 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.916 
Switching outliers to nearest non-outliers
  outliers start: 28
  outliers final: 26
  residues processed: 2
  average time/residue: 0.1003
  time to fit residues: 1.5291
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 86 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0170
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS
B  32 GLN
B  35 ASN
B 175 GLN
B 220 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.4764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8467  Z= 0.161
  Angle     :  0.495   9.409  11489  Z= 0.258
  Chirality :  0.041   0.133   1306
  Planarity :  0.003   0.030   1450
  Dihedral  :  4.479  50.839   1280
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.61 %
    Favored  : 75.56 %
  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:  0.96 (0.26), residues: 1032
  helix:  1.73 (0.27), residues: 394
  sheet:  0.57 (0.33), residues: 233
  loop : -0.36 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 209 
   PHE   0.011   0.001   PHE A  74 
   TYR   0.016   0.001   TYR R 129 
   ARG   0.007   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.896 
Fit side-chains
  outliers start: 34
  outliers final: 30
  residues processed: 160
  average time/residue: 1.3044
  time to fit residues: 221.5805
Evaluate side-chains
  155 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.976 
Switching outliers to nearest non-outliers
  outliers start: 30
  outliers final: 26
  residues processed: 4
  average time/residue: 0.4557
  time to fit residues: 3.4012
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 93 optimal weight:    0.0570
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   chunk 24 optimal weight:    0.0870
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  52 GLN
B  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8467  Z= 0.124
  Angle     :  0.472   9.891  11489  Z= 0.245
  Chirality :  0.040   0.136   1306
  Planarity :  0.003   0.029   1450
  Dihedral  :  4.268  48.928   1280
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.17 %
    Favored  : 75.56 %
  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:  1.07 (0.26), residues: 1032
  helix:  1.94 (0.27), residues: 394
  sheet:  0.59 (0.33), residues: 236
  loop : -0.41 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP B  82 
   HIS   0.004   0.001   HIS A 209 
   PHE   0.010   0.001   PHE A  74 
   TYR   0.016   0.001   TYR R 129 
   ARG   0.007   0.000   ARG A  15 

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

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

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2064 Ramachandran restraints generated.
    1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
  outliers start: 29
  outliers final: 23
  residues processed: 162
  average time/residue: 1.2542
  time to fit residues: 216.0903
Evaluate side-chains
  151 residues out of total 888 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.961 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 23
  residues processed: 0
  time to fit residues: 1.3521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 298 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.156234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.121901 restraints weight = 8869.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.91
r_work: 0.3320 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8467  Z= 0.152
  Angle     :  0.479   6.991  11489  Z= 0.251
  Chirality :  0.041   0.151   1306
  Planarity :  0.003   0.029   1450
  Dihedral  :  4.405  49.506   1280
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.96 %
    Favored  : 74.77 %
  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 (0.26), residues: 1032
  helix:  1.83 (0.27), residues: 400
  sheet:  0.53 (0.32), residues: 243
  loop : -0.37 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 209 
   PHE   0.011   0.001   PHE B 151 
   TYR   0.016   0.001   TYR B 124 
   ARG   0.007   0.000   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3961.33 seconds
wall clock time: 70 minutes 47.77 seconds (4247.77 seconds total)