Starting phenix.real_space_refine
on Mon Mar 11 12:20:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/03_2024/7xov_33360_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/03_2024/7xov_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_33360/03_2024/7xov_33360.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/03_2024/7xov_33360.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/03_2024/7xov_33360_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xov_33360/03_2024/7xov_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-dev-5265/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: 5.14, per 1000 atoms: 0.63
  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: 3.35
  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: 1.59
  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: 2.34

  Time building geometry restraints manager: 3.62 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:             0.540
  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:          2.170
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     26.390
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.190
-------------------------------------------------------------------------------
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  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.4362 (p0) cc_final: 0.2845 (p0)
REVERT: G   21 MET cc_start: 0.3505 (mtm) cc_final: 0.3188 (ttt)
  outliers start: 8
  outliers final: 3
  residues processed: 88
  average time/residue: 1.3007
  time to fit residues: 121.8979
Evaluate side-chains
  60 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  336 ARG
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:    0.9980
   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:    0.9580

-------------------------------------------------------------------------------
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: 0.1121
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8381  Z= 0.240
  Angle     :  0.726   8.122  11346  Z= 0.395
  Chirality :  0.047   0.213   1282
  Planarity :  0.006   0.069   1440
  Dihedral  :  7.243  81.681   1163
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.46 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.05 %
    Favored  : 92.83 %
  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:  0.76 (0.26), residues: 1018
  helix:  1.07 (0.26), residues: 379
  sheet:  1.03 (0.33), residues: 217
  loop : -0.21 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP R 326 
 HIS   0.006   0.002   HIS R 157 
 PHE   0.021   0.003   PHE R 212 
 TYR   0.017   0.002   TYR B 124 
 ARG   0.006   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
  79 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 MET cc_start: 0.2091 (mpt) cc_final: -0.1053 (ttt)
REVERT: G   21 MET cc_start: 0.3423 (mtm) cc_final: 0.2455 (ptm)
  outliers start: 10
  outliers final: 3
  residues processed: 74
  average time/residue: 1.2948
  time to fit residues: 102.2552
Evaluate side-chains
  54 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain R residue  119 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0570
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
** R  69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1995
moved from start:          0.5834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   8381  Z= 0.235
  Angle     :  0.706  10.712  11346  Z= 0.373
  Chirality :  0.046   0.353   1282
  Planarity :  0.006   0.078   1440
  Dihedral  :  6.582  86.809   1157
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  7.61 %
    Favored  : 90.48 %
  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:  0.66 (0.27), residues: 1018
  helix:  1.07 (0.26), residues: 378
  sheet:  0.82 (0.35), residues: 206
  loop : -0.22 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP R 166 
 HIS   0.007   0.001   HIS B  91 
 PHE   0.036   0.002   PHE R 198 
 TYR   0.025   0.002   TYR N  94 
 ARG   0.010   0.001   ARG B  49 

*********************** 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
  99 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.3974 (mtm) cc_final: 0.3376 (ttt)
  outliers start: 17
  outliers final: 6
  residues processed: 92
  average time/residue: 0.9952
  time to fit residues: 98.9815
Evaluate side-chains
  68 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  180 SER
Chi-restraints excluded: chain R residue  195 MET
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.0070
   chunk 47 optimal weight:    7.9990
   chunk 10 optimal weight:    0.3980
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.6000

-------------------------------------------------------------------------------
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  13 GLN
B 259 GLN
B 340 ASN
R  69 ASN
R 153 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2630
moved from start:          0.7431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8381  Z= 0.215
  Angle     :  0.649   8.341  11346  Z= 0.340
  Chirality :  0.043   0.182   1282
  Planarity :  0.005   0.063   1440
  Dihedral  :  5.799  59.778   1157
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.08 %
    Favored  : 88.24 %
  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:  0.44 (0.26), residues: 1018
  helix:  1.04 (0.27), residues: 381
  sheet:  0.53 (0.34), residues: 208
  loop : -0.42 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.007   0.001   HIS B  91 
 PHE   0.040   0.002   PHE N  68 
 TYR   0.014   0.002   TYR R  48 
 ARG   0.005   0.001   ARG B   8 

*********************** 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
  95 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A  293 LYS cc_start: 0.5220 (mmtp) cc_final: 0.4510 (tptt)
REVERT: B  188 MET cc_start: 0.3430 (mpt) cc_final: 0.3036 (mmm)
REVERT: B  262 MET cc_start: 0.0218 (tpp) cc_final: -0.0190 (tpp)
REVERT: B  325 MET cc_start: 0.2655 (ttt) cc_final: 0.2292 (mmt)
REVERT: G   21 MET cc_start: 0.3892 (mtm) cc_final: 0.3481 (ttt)
REVERT: R  121 MET cc_start: 0.4144 (tpt) cc_final: 0.3577 (tpp)
REVERT: R  166 TRP cc_start: 0.6014 (m100) cc_final: 0.4697 (m100)
  outliers start: 15
  outliers final: 6
  residues processed: 92
  average time/residue: 0.9111
  time to fit residues: 91.3534
Evaluate side-chains
  65 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3520
moved from start:          0.9782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8381  Z= 0.226
  Angle     :  0.700  10.641  11346  Z= 0.362
  Chirality :  0.046   0.266   1282
  Planarity :  0.006   0.105   1440
  Dihedral  :  5.841  57.410   1157
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 10.86 %
    Favored  : 85.89 %
  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:  0.36 (0.27), residues: 1018
  helix:  0.91 (0.27), residues: 384
  sheet:  0.70 (0.36), residues: 198
  loop : -0.50 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP B  63 
 HIS   0.010   0.002   HIS B  54 
 PHE   0.019   0.002   PHE G  61 
 TYR   0.019   0.002   TYR B 111 
 ARG   0.010   0.001   ARG N 118 

*********************** 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
  110 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.0422 (tpp) cc_final: 0.0182 (tpp)
REVERT: B  325 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3499 (mmt)
REVERT: R  226 MET cc_start: 0.6428 (tpp) cc_final: 0.5571 (ttt)
  outliers start: 29
  outliers final: 10
  residues processed: 99
  average time/residue: 0.8850
  time to fit residues: 95.5821
Evaluate side-chains
  70 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue  118 THR
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9980
   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**
B  91 HIS
R 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4197
moved from start:          1.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8381  Z= 0.226
  Angle     :  0.663   9.151  11346  Z= 0.345
  Chirality :  0.044   0.173   1282
  Planarity :  0.005   0.067   1440
  Dihedral  :  5.358  55.170   1155
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.11 %
    Favored  : 83.43 %
  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:  0.43 (0.27), residues: 1018
  helix:  1.17 (0.27), residues: 374
  sheet:  0.51 (0.36), residues: 207
  loop : -0.54 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  63 
 HIS   0.008   0.001   HIS B  62 
 PHE   0.029   0.002   PHE N  68 
 TYR   0.019   0.002   TYR R 119 
 ARG   0.008   0.001   ARG B  49 

*********************** 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
  109 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.5851 (mttt) cc_final: 0.5551 (tppt)
REVERT: A  227 GLN cc_start: 0.3995 (OUTLIER) cc_final: 0.2730 (mt0)
REVERT: B  211 TRP cc_start: 0.1037 (OUTLIER) cc_final: 0.0671 (t60)
REVERT: B  217 MET cc_start: 0.1091 (tpt) cc_final: 0.0837 (tpt)
REVERT: B  262 MET cc_start: 0.0220 (tpp) cc_final: -0.0178 (tpp)
REVERT: B  286 LEU cc_start: 0.7712 (mm) cc_final: 0.7492 (mm)
REVERT: B  290 ASP cc_start: 0.4247 (m-30) cc_final: 0.3749 (m-30)
REVERT: B  325 MET cc_start: 0.4695 (ttt) cc_final: 0.4182 (tpp)
REVERT: N   11 LEU cc_start: 0.3550 (tt) cc_final: 0.3346 (tm)
REVERT: R  182 LEU cc_start: 0.5212 (pt) cc_final: 0.4762 (mm)
REVERT: R  346 ARG cc_start: 0.3782 (tpt170) cc_final: 0.2876 (tpp-160)
REVERT: R  372 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6525 (t80)
  outliers start: 22
  outliers final: 9
  residues processed: 103
  average time/residue: 0.8380
  time to fit residues: 94.4880
Evaluate side-chains
  85 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain R residue   87 ASP
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 71 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0980
   chunk 60 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5182
moved from start:          1.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8381  Z= 0.315
  Angle     :  0.834  12.773  11346  Z= 0.433
  Chirality :  0.050   0.296   1282
  Planarity :  0.006   0.078   1440
  Dihedral  :  5.915  52.268   1155
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.23 %
    Favored  : 81.86 %
  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: -0.19 (0.27), residues: 1018
  helix:  0.50 (0.27), residues: 377
  sheet:  0.13 (0.36), residues: 215
  loop : -0.73 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP B  63 
 HIS   0.011   0.002   HIS A  41 
 PHE   0.030   0.002   PHE N 103 
 TYR   0.020   0.003   TYR B 289 
 ARG   0.006   0.001   ARG R 139 

*********************** 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
  129 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   60 MET cc_start: 0.1622 (tmt) cc_final: 0.0667 (tmt)
REVERT: A  238 PHE cc_start: 0.1792 (m-80) cc_final: 0.1574 (m-80)
REVERT: G   48 ASP cc_start: 0.7413 (t0) cc_final: 0.6711 (p0)
REVERT: N   34 MET cc_start: 0.2636 (mpm) cc_final: 0.2402 (mmp)
REVERT: R  182 LEU cc_start: 0.5746 (pt) cc_final: 0.5349 (mm)
REVERT: R  195 MET cc_start: 0.2854 (tpp) cc_final: 0.2212 (ttp)
REVERT: R  226 MET cc_start: 0.6806 (ttm) cc_final: 0.6584 (ttp)
REVERT: R  237 TYR cc_start: 0.6745 (t80) cc_final: 0.6302 (t80)
REVERT: R  346 ARG cc_start: 0.4654 (tpt170) cc_final: 0.3404 (tpp-160)
REVERT: R  372 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6960 (t80)
  outliers start: 26
  outliers final: 10
  residues processed: 122
  average time/residue: 0.8679
  time to fit residues: 115.3904
Evaluate side-chains
  93 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  365 VAL
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0170
   chunk 61 optimal weight:    0.0040
   chunk 66 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0270
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0670
   overall best weight:    0.0826

-------------------------------------------------------------------------------
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 237 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 210 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5069
moved from start:          1.5320

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= 0.173
  Angle     :  0.643  10.119  11346  Z= 0.327
  Chirality :  0.042   0.190   1282
  Planarity :  0.005   0.083   1440
  Dihedral  :  5.184  47.391   1155
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.65 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.15 %
    Favored  : 78.95 %
  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:  0.32 (0.27), residues: 1018
  helix:  1.21 (0.27), residues: 380
  sheet:  0.40 (0.36), residues: 210
  loop : -0.74 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B  99 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.013   0.001   PHE A 238 
 TYR   0.015   0.001   TYR A 360 
 ARG   0.006   0.000   ARG B  68 

*********************** 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
  106 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.1284 (tmt) cc_final: 0.0655 (tmt)
REVERT: G   48 ASP cc_start: 0.7353 (t0) cc_final: 0.6626 (p0)
REVERT: R  195 MET cc_start: 0.2914 (tpp) cc_final: 0.2351 (ttp)
REVERT: R  237 TYR cc_start: 0.6512 (t80) cc_final: 0.6096 (t80)
REVERT: R  336 ARG cc_start: 0.4799 (OUTLIER) cc_final: 0.4033 (ttt180)
REVERT: R  346 ARG cc_start: 0.4651 (tpt170) cc_final: 0.3358 (tpp-160)
REVERT: R  372 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6950 (t80)
  outliers start: 17
  outliers final: 5
  residues processed: 101
  average time/residue: 0.8960
  time to fit residues: 98.5113
Evaluate side-chains
  79 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  336 ARG
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0470
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 59 optimal weight:    0.4980
   chunk 95 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 340 ASN
R 206 GLN
R 304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5241
moved from start:          1.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8381  Z= 0.192
  Angle     :  0.665  12.138  11346  Z= 0.340
  Chirality :  0.043   0.225   1282
  Planarity :  0.005   0.074   1440
  Dihedral  :  5.070  48.619   1155
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.83 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.82 %
    Favored  : 78.39 %
  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:  0.26 (0.27), residues: 1018
  helix:  1.03 (0.27), residues: 392
  sheet:  0.39 (0.36), residues: 208
  loop : -0.69 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  99 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.030   0.001   PHE R 198 
 TYR   0.016   0.002   TYR A 391 
 ARG   0.009   0.000   ARG B  68 

*********************** 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
  99 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.1273 (tmt) cc_final: 0.0560 (tmt)
REVERT: A  238 PHE cc_start: 0.4302 (m-80) cc_final: 0.3558 (m-80)
REVERT: B  217 MET cc_start: 0.3905 (tpt) cc_final: 0.2581 (ppp)
REVERT: R  237 TYR cc_start: 0.6761 (t80) cc_final: 0.6321 (t80)
REVERT: R  336 ARG cc_start: 0.4838 (ttp-170) cc_final: 0.4178 (ttt-90)
REVERT: R  346 ARG cc_start: 0.4829 (tpt170) cc_final: 0.3536 (tpp-160)
REVERT: R  372 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7119 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 96
  average time/residue: 0.9458
  time to fit residues: 99.0343
Evaluate side-chains
  85 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  121 MET
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 92 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0970
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5347
moved from start:          1.6402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8381  Z= 0.193
  Angle     :  0.650  10.742  11346  Z= 0.332
  Chirality :  0.044   0.214   1282
  Planarity :  0.005   0.073   1440
  Dihedral  :  5.023  49.065   1155
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.83 %
    Favored  : 77.38 %
  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:  0.22 (0.27), residues: 1018
  helix:  1.06 (0.27), residues: 393
  sheet:  0.38 (0.36), residues: 203
  loop : -0.79 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  99 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.035   0.001   PHE A 238 
 TYR   0.014   0.002   TYR A 391 
 ARG   0.009   0.000   ARG B  68 

********************** 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
  102 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.1199 (tmt) cc_final: 0.0451 (tmt)
REVERT: B  217 MET cc_start: 0.4134 (tpt) cc_final: 0.2894 (ppp)
REVERT: N   34 MET cc_start: 0.2826 (mpm) cc_final: 0.1985 (tpp)
REVERT: R  237 TYR cc_start: 0.6573 (t80) cc_final: 0.6183 (t80)
REVERT: R  336 ARG cc_start: 0.4889 (ttp-170) cc_final: 0.4238 (ttt-90)
REVERT: R  346 ARG cc_start: 0.4878 (tpt170) cc_final: 0.3541 (tpp-160)
REVERT: R  372 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.7031 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 98
  average time/residue: 0.8708
  time to fit residues: 93.4772
Evaluate side-chains
  86 residues out of total 893 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 82 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 4 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0040
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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 357 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.285715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.235991 restraints weight = 9264.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4593 rms_B_bonded: 2.87
r_work: 0.4466 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5839
moved from start:          1.6831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8381  Z= 0.169
  Angle     :  0.629  10.505  11346  Z= 0.321
  Chirality :  0.043   0.207   1282
  Planarity :  0.004   0.049   1440
  Dihedral  :  4.828  47.863   1155
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.93 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 21.95 %
    Favored  : 76.15 %
  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:  0.33 (0.27), residues: 1018
  helix:  1.18 (0.28), residues: 395
  sheet:  0.27 (0.35), residues: 210
  loop : -0.69 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  63 
 HIS   0.003   0.001   HIS A 362 
 PHE   0.024   0.001   PHE R 198 
 TYR   0.014   0.001   TYR R 176 
 ARG   0.008   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2693.72 seconds
wall clock time: 49 minutes 10.58 seconds (2950.58 seconds total)