Starting phenix.real_space_refine
on Fri Dec  8 11:24:28 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/12_2023/7xov_33360_trim_updated.pdb"
  }
  resolution = 3.0
  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=   0.007
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: 5
    Type Number    sf(0)   Gaussians
     S      61      5.16       5
     Cl      1      4.86       5
     C    5217      2.51       5
     N    1427      2.21       5
     O    1512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R TYR  176": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG  336": "NH1" <-> "NH2"
    Residue "R TYR  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  344": "OE1" <-> "OE2"
  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: 8218
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1884
          Classifications: {'peptide': 227}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118}
    Chain: "R"
      Number of atoms: 2336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2336
          Unusual residues: {'IA1': 1}
          Classifications: {'peptide': 288, 'undetermined': 1, 'water': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 276, None: 2}
            Not linked:
              pdbres="PHE R 385 "
              pdbres="IA1 R 501 "
            Not linked:
              pdbres="IA1 R 501 "
              pdbres="HOH R 601 "
          Chain breaks: 1
  Time building chain proxies: 4.92, per 1000 atoms: 0.60
  Number of scatterers: 8218
  At special positions: 0
  Unit cell: (90.246, 95.316, 134.862, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      61     16.00
     O    1512      8.00
     N    1427      7.00
     C    5217      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.60
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      38.5% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.515A  pdb=" N   LYS A  17 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ARG A  38 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 59
    Processing helix  chain 'A' and resid 235 through 238
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 332 through 351
      removed outlier: 4.027A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
      removed outlier: 3.575A  pdb=" N   ILE A 383 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.983A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 32
      No H-bonds generated for 'chain 'B' and resid 30 through 32'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 4.400A  pdb=" N   ARG G  13 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL G  16 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'G' and resid 56 through 58
      No H-bonds generated for 'chain 'G' and resid 56 through 58'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'R' and resid 44 through 68
      removed outlier: 3.548A  pdb=" N   ILE R  67 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 94
    Processing helix  chain 'R' and resid 99 through 104
      removed outlier: 3.551A  pdb=" N   LEU R 103 " --> pdb=" O   LEU R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 144
    Processing helix  chain 'R' and resid 146 through 152
      removed outlier: 4.351A  pdb=" N   VAL R 151 " --> pdb=" O   LEU R 147 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TRP R 152 " --> pdb=" O   GLN R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 172
      removed outlier: 4.140A  pdb=" N   LYS R 160 " --> pdb=" O   SER R 156 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   THR R 171 " --> pdb=" O   CYS R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 176
      No H-bonds generated for 'chain 'R' and resid 174 through 176'
    Processing helix  chain 'R' and resid 204 through 217
      removed outlier: 3.702A  pdb=" N   TRP R 209 " --> pdb=" O   GLN R 206 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE R 216 " --> pdb=" O   LEU R 213 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R 217 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 243
    Processing helix  chain 'R' and resid 302 through 338
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 340 through 349
      removed outlier: 3.632A  pdb=" N   GLY R 349 " --> pdb=" O   ARG R 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 352 through 370
      removed outlier: 3.804A  pdb=" N   SER R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   SER R 363 " --> pdb=" O   SER R 359 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS R 364 " --> pdb=" O   TYR R 360 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 379 through 384
    Processing sheet with id=  A, first strand: chain 'A' and resid 359 through 363
      removed outlier: 7.146A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.701A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ASN A 218 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   HIS A 220 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   GLY A  47 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.838A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.246A  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: 6.902A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.364A  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 152
      removed outlier: 6.856A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.116A  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: 6.616A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 5.867A  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: 6.749A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.701A  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: 6.522A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.870A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 122 through 124
      removed outlier: 5.837A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'R' and resid 180 through 182

    390 hydrogen bonds defined for protein.
    939 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: 2.36

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1400
        1.31 -     1.44: 2275
        1.44 -     1.57: 4588
        1.57 -     1.70: 29
        1.70 -     1.83: 89
  Bond restraints: 8381
  Sorted by residual:
  bond pdb=" C19 IA1 R 501 "
       pdb=" S2  IA1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.731  1.520  0.211 2.00e-02 2.50e+03 1.11e+02
  bond pdb=" C20 IA1 R 501 "
       pdb=" N8  IA1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.372  1.556 -0.184 2.00e-02 2.50e+03 8.44e+01
  bond pdb=" C21 IA1 R 501 "
       pdb=" S2  IA1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.727  1.551  0.176 2.00e-02 2.50e+03 7.71e+01
  bond pdb=" C25 IA1 R 501 "
       pdb=" C32 IA1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.404  1.565 -0.161 2.00e-02 2.50e+03 6.47e+01
  bond pdb=" C23 IA1 R 501 "
       pdb=" C30 IA1 R 501 "
    ideal  model  delta    sigma   weight residual
    1.414  1.572 -0.158 2.00e-02 2.50e+03 6.26e+01
  ... (remaining 8376 not shown)

  Histogram of bond angle deviations from ideal:
       96.53 -   108.16: 648
      108.16 -   119.80: 6942
      119.80 -   131.43: 3730
      131.43 -   143.07: 24
      143.07 -   154.71: 2
  Bond angle restraints: 11346
  Sorted by residual:
  angle pdb=" C   LYS R 187 "
        pdb=" N   ASN R 188 "
        pdb=" CA  ASN R 188 "
      ideal   model   delta    sigma   weight residual
     120.72  154.71  -33.99 1.67e+00 3.59e-01 4.14e+02
  angle pdb=" C   THR N  28 "
        pdb=" N   PHE N  29 "
        pdb=" CA  PHE N  29 "
      ideal   model   delta    sigma   weight residual
     122.85   96.53   26.32 1.39e+00 5.18e-01 3.59e+02
  angle pdb=" C   GLN N 120 "
        pdb=" N   GLY N 121 "
        pdb=" CA  GLY N 121 "
      ideal   model   delta    sigma   weight residual
     121.70  151.55  -29.85 1.80e+00 3.09e-01 2.75e+02
  angle pdb=" N   GLU A 230 "
        pdb=" CA  GLU A 230 "
        pdb=" C   GLU A 230 "
      ideal   model   delta    sigma   weight residual
     111.28  123.26  -11.98 1.09e+00 8.42e-01 1.21e+02
  angle pdb=" N   SER N  30 "
        pdb=" CA  SER N  30 "
        pdb=" C   SER N  30 "
      ideal   model   delta    sigma   weight residual
     114.39  100.64   13.75 1.45e+00 4.76e-01 8.99e+01
  ... (remaining 11341 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 4816
       17.11 -    34.22: 148
       34.22 -    51.34: 32
       51.34 -    68.45: 26
       68.45 -    85.56: 6
  Dihedral angle restraints: 5028
    sinusoidal: 2012
      harmonic: 3016
  Sorted by residual:
  dihedral pdb=" CA  ASP A 223 "
           pdb=" C   ASP A 223 "
           pdb=" N   VAL A 224 "
           pdb=" CA  VAL A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.20  -38.80     0      5.00e+00 4.00e-02 6.02e+01
  dihedral pdb=" CA  ASN N  84 "
           pdb=" C   ASN N  84 "
           pdb=" N   SER N  85 "
           pdb=" CA  SER N  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.28  -34.72     0      5.00e+00 4.00e-02 4.82e+01
  dihedral pdb=" CB  CYS R 114 "
           pdb=" SG  CYS R 114 "
           pdb=" SG  CYS R 196 "
           pdb=" CB  CYS R 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.12   58.12     1      1.00e+01 1.00e-02 4.53e+01
  ... (remaining 5025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 823
       0.080 -    0.160: 348
       0.160 -    0.239: 95
       0.239 -    0.319: 15
       0.319 -    0.399: 1
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" CA  GLU A 230 "
            pdb=" N   GLU A 230 "
            pdb=" C   GLU A 230 "
            pdb=" CB  GLU A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" CA  TYR B 111 "
            pdb=" N   TYR B 111 "
            pdb=" C   TYR B 111 "
            pdb=" CB  TYR B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  ILE B 171 "
            pdb=" N   ILE B 171 "
            pdb=" C   ILE B 171 "
            pdb=" CB  ILE B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.18e+00
  ... (remaining 1279 not shown)

  Planarity restraints: 1440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 237 "    0.072 2.00e-02 2.50e+03   1.48e-01 2.19e+02
        pdb=" C   ASN B 237 "   -0.256 2.00e-02 2.50e+03
        pdb=" O   ASN B 237 "    0.096 2.00e-02 2.50e+03
        pdb=" N   GLY B 238 "    0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B  66 "    0.067 2.00e-02 2.50e+03   1.44e-01 2.08e+02
        pdb=" C   ASP B  66 "   -0.249 2.00e-02 2.50e+03
        pdb=" O   ASP B  66 "    0.098 2.00e-02 2.50e+03
        pdb=" N   SER B  67 "    0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 276 "    0.066 2.00e-02 2.50e+03   1.44e-01 2.07e+02
        pdb=" C   ILE A 276 "   -0.249 2.00e-02 2.50e+03
        pdb=" O   ILE A 276 "    0.099 2.00e-02 2.50e+03
        pdb=" N   TRP A 277 "    0.084 2.00e-02 2.50e+03
  ... (remaining 1437 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2598
        2.84 -     3.35: 7991
        3.35 -     3.87: 13718
        3.87 -     4.38: 16957
        4.38 -     4.90: 27124
  Nonbonded interactions: 68388
  Sorted by model distance:
  nonbonded pdb=" O   THR N  28 "
            pdb=" CA  PHE N  29 "
     model   vdw
     2.322 2.776
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.342 2.520
  nonbonded pdb=" N   SER N  30 "
            pdb=" N   ASN N  31 "
     model   vdw
     2.344 2.560
  nonbonded pdb=" CD1 LEU R 347 "
            pdb=" C39 IA1 R 501 "
     model   vdw
     2.346 3.880
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.352 2.440
  ... (remaining 68383 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.610
  Check model and map are aligned:         0.130
  Set scattering table:                    0.090
  Process input model:                     26.740
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0298
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      :  0.019   0.211   8381  Z= 1.280
  Angle     :  1.842  33.986  11346  Z= 1.238
  Chirality :  0.091   0.399   1282
  Planarity :  0.017   0.148   1440
  Dihedral  : 10.850  85.562   3063
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.05 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  1.01 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.40 %

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:  0.50 (0.25), residues: 1018
  helix: -0.26 (0.23), residues: 388
  sheet:  1.46 (0.33), residues: 215
  loop :  0.54 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.050   0.011   TRP B  99 
   HIS   0.007   0.003   HIS B 183 
   PHE   0.050   0.006   PHE N  27 
   TYR   0.085   0.009   TYR R 179 
   ARG   0.008   0.001   ARG N  72 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 88
  average time/residue: 1.3720
  time to fit residues: 128.1519
Evaluate side-chains
  59 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.820 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 0
  time to fit residues: 1.2293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 340 ASN
R 131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1111
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8381  Z= 0.246
  Angle     :  0.730   8.308  11346  Z= 0.398
  Chirality :  0.047   0.213   1282
  Planarity :  0.006   0.070   1440
  Dihedral  :  6.819  81.239   1155
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.55 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.16 %
    Favored  : 92.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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:  0.79 (0.26), residues: 1018
  helix:  1.08 (0.26), residues: 379
  sheet:  1.07 (0.33), residues: 217
  loop : -0.19 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.003   TRP R 326 
   HIS   0.005   0.002   HIS R 157 
   PHE   0.021   0.003   PHE R 212 
   TYR   0.017   0.002   TYR B 124 
   ARG   0.007   0.001   ARG R  73 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
  outliers start: 11
  outliers final: 5
  residues processed: 72
  average time/residue: 1.2530
  time to fit residues: 96.5676
Evaluate side-chains
  56 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.881 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 1.1688
  time to fit residues: 2.5506
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
R  69 ASN
R 207 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2054
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   8381  Z= 0.277
  Angle     :  0.714   7.930  11346  Z= 0.380
  Chirality :  0.045   0.194   1282
  Planarity :  0.006   0.075   1440
  Dihedral  :  6.523  90.333   1155
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  7.73 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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:  0.57 (0.27), residues: 1018
  helix:  0.96 (0.26), residues: 378
  sheet:  0.74 (0.35), residues: 213
  loop : -0.22 (0.32), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.003   TRP R 166 
   HIS   0.006   0.001   HIS B  91 
   PHE   0.029   0.002   PHE R 198 
   TYR   0.013   0.002   TYR R 176 
   ARG   0.009   0.001   ARG G  13 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 9
  residues processed: 90
  average time/residue: 1.0706
  time to fit residues: 104.3078
Evaluate side-chains
  70 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.927 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 6
  residues processed: 4
  average time/residue: 0.4143
  time to fit residues: 3.2836
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 48 optimal weight:    0.2980
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0040
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  13 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 153 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2511
moved from start:          0.7205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8381  Z= 0.190
  Angle     :  0.633   9.272  11346  Z= 0.333
  Chirality :  0.043   0.168   1282
  Planarity :  0.005   0.063   1440
  Dihedral  :  5.699  67.719   1155
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.07 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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:  0.57 (0.27), residues: 1018
  helix:  1.14 (0.27), residues: 382
  sheet:  0.51 (0.34), residues: 212
  loop : -0.31 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B  82 
   HIS   0.005   0.001   HIS B  62 
   PHE   0.024   0.002   PHE R 198 
   TYR   0.021   0.001   TYR B  59 
   ARG   0.007   0.001   ARG B 197 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.938 
Fit side-chains
  outliers start: 22
  outliers final: 11
  residues processed: 89
  average time/residue: 0.9354
  time to fit residues: 91.0536
Evaluate side-chains
  70 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.977 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 7
  residues processed: 4
  average time/residue: 0.6990
  time to fit residues: 4.3898
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4387
moved from start:          1.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.165   8381  Z= 0.405
  Angle     :  0.946  12.292  11346  Z= 0.497
  Chirality :  0.053   0.451   1282
  Planarity :  0.007   0.091   1440
  Dihedral  :  6.299  48.956   1155
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 10.75 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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: -0.65 (0.25), residues: 1018
  helix: -0.04 (0.25), residues: 383
  sheet: -0.09 (0.33), residues: 213
  loop : -0.83 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.054   0.005   TRP R 166 
   HIS   0.020   0.002   HIS B 311 
   PHE   0.022   0.003   PHE B 235 
   TYR   0.022   0.003   TYR R 140 
   ARG   0.014   0.001   ARG B  49 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
  outliers start: 37
  outliers final: 13
  residues processed: 131
  average time/residue: 0.9094
  time to fit residues: 129.4707
Evaluate side-chains
  82 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.910 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 12
  residues processed: 1
  average time/residue: 0.0768
  time to fit residues: 1.4944
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
R 207 GLN
R 304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4625
moved from start:          1.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8381  Z= 0.233
  Angle     :  0.684   9.868  11346  Z= 0.353
  Chirality :  0.044   0.205   1282
  Planarity :  0.005   0.066   1440
  Dihedral  :  5.364  48.398   1155
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.45 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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: -0.11 (0.26), residues: 1018
  helix:  0.75 (0.27), residues: 386
  sheet: -0.17 (0.34), residues: 208
  loop : -0.67 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B 339 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.024   0.002   PHE B 180 
   TYR   0.021   0.002   TYR R 119 
   ARG   0.005   0.001   ARG B  96 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
  outliers start: 30
  outliers final: 13
  residues processed: 106
  average time/residue: 0.8063
  time to fit residues: 94.1383
Evaluate side-chains
  78 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.946 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.7334
  time to fit residues: 3.7837
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   chunk 82 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
R 210 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5061
moved from start:          1.4683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8381  Z= 0.240
  Angle     :  0.701  10.998  11346  Z= 0.362
  Chirality :  0.045   0.241   1282
  Planarity :  0.005   0.074   1440
  Dihedral  :  5.294  46.758   1155
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.81 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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: -0.05 (0.27), residues: 1018
  helix:  0.72 (0.27), residues: 395
  sheet: -0.10 (0.33), residues: 217
  loop : -0.61 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP A 277 
   HIS   0.008   0.001   HIS B  54 
   PHE   0.031   0.002   PHE A 219 
   TYR   0.013   0.002   TYR A 360 
   ARG   0.008   0.001   ARG B  49 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.918 
Fit side-chains
  outliers start: 30
  outliers final: 14
  residues processed: 108
  average time/residue: 0.9058
  time to fit residues: 106.8430
Evaluate side-chains
  85 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.902 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 11
  residues processed: 3
  average time/residue: 0.7416
  time to fit residues: 3.7464
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0040
   chunk 66 optimal weight:    0.7980
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5188
moved from start:          1.5446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8381  Z= 0.198
  Angle     :  0.651   9.570  11346  Z= 0.330
  Chirality :  0.042   0.168   1282
  Planarity :  0.005   0.070   1440
  Dihedral  :  5.174  48.512   1155
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.44 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.48 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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:  0.11 (0.27), residues: 1018
  helix:  0.97 (0.27), residues: 391
  sheet:  0.10 (0.34), residues: 208
  loop : -0.72 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B 339 
   HIS   0.009   0.001   HIS B  54 
   PHE   0.020   0.002   PHE A 219 
   TYR   0.016   0.001   TYR N 115 
   ARG   0.007   0.000   ARG B 197 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
  outliers start: 25
  outliers final: 15
  residues processed: 93
  average time/residue: 0.8653
  time to fit residues: 88.4103
Evaluate side-chains
  81 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 14
  residues processed: 1
  average time/residue: 0.0766
  time to fit residues: 1.4582
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 93 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
R 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5412
moved from start:          1.6485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8381  Z= 0.201
  Angle     :  0.680  10.516  11346  Z= 0.343
  Chirality :  0.044   0.182   1282
  Planarity :  0.005   0.078   1440
  Dihedral  :  5.182  47.799   1155
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.83 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.04 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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:  0.12 (0.27), residues: 1018
  helix:  1.07 (0.27), residues: 390
  sheet: -0.02 (0.34), residues: 209
  loop : -0.74 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 277 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.017   0.002   PHE R 198 
   TYR   0.035   0.002   TYR B 264 
   ARG   0.018   0.001   ARG A 232 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 15
  residues processed: 109
  average time/residue: 1.0285
  time to fit residues: 121.2942
Evaluate side-chains
  87 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.877 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 14
  residues processed: 1
  average time/residue: 0.0776
  time to fit residues: 1.5762
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 92 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5554
moved from start:          1.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8381  Z= 0.206
  Angle     :  0.681  10.279  11346  Z= 0.351
  Chirality :  0.044   0.203   1282
  Planarity :  0.004   0.043   1440
  Dihedral  :  5.167  47.553   1155
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.16 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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 (0.27), residues: 1018
  helix:  1.17 (0.28), residues: 383
  sheet:  0.06 (0.34), residues: 208
  loop : -0.90 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 277 
   HIS   0.005   0.001   HIS B  54 
   PHE   0.017   0.002   PHE R 198 
   TYR   0.014   0.002   TYR B  85 
   ARG   0.007   0.001   ARG B 197 

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 17
  residues processed: 97
  average time/residue: 1.0199
  time to fit residues: 106.9718
Evaluate side-chains
  91 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.870 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 16
  residues processed: 1
  average time/residue: 0.0881
  time to fit residues: 1.3662
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0870
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0370
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4900 r_free = 0.4900 target = 0.276941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.225212 restraints weight = 9051.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.4518 rms_B_bonded: 2.85
r_work: 0.4388 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6048
moved from start:          1.7769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8381  Z= 0.174
  Angle     :  0.648  10.815  11346  Z= 0.329
  Chirality :  0.043   0.197   1282
  Planarity :  0.004   0.048   1440
  Dihedral  :  5.080  46.684   1155
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.83 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 22.06 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    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:  0.25 (0.27), residues: 1018
  helix:  1.40 (0.28), residues: 377
  sheet: -0.09 (0.34), residues: 214
  loop : -0.77 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B 211 
   HIS   0.004   0.001   HIS B  54 
   PHE   0.017   0.001   PHE R 198 
   TYR   0.010   0.001   TYR N 115 
   ARG   0.009   0.000   ARG B  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2737.21 seconds
wall clock time: 49 minutes 53.18 seconds (2993.18 seconds total)