Starting phenix.real_space_refine
on Wed Sep 17 10:33:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_33360_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_33360_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_33360_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_33360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xov_33360/09_2025/7xov_33360.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8218
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2293
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 11, 'TRANS': 276}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'IA1': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.24
  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  - 3.00
        Amino acid           : True  - 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: 0.72
  Conformation dependent library (CDL) restraints added in 429.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      42.1% alpha, 21.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 4.027A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 389
      removed outlier: 3.623A  pdb=" N   ASN A 377 " --> pdb=" O   ARG A 373 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 392
      No H-bonds generated for 'chain 'A' and resid 390 through 392'
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.920A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
      removed outlier: 4.403A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 43 through 69
      removed outlier: 3.720A  pdb=" N   LEU R  47 " --> pdb=" O   VAL R  43 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE R  67 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 95
      removed outlier: 3.913A  pdb=" N   MET R  95 " --> pdb=" O   CYS R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 98 through 105
      removed outlier: 3.551A  pdb=" N   LEU R 103 " --> pdb=" O   LEU R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 110 through 145
    Processing helix  chain 'R' and resid 145 through 153
      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 154 through 173
      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 204 through 218
    Processing helix  chain 'R' and resid 218 through 244
    Processing helix  chain 'R' and resid 302 through 339
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 339 through 350
      removed outlier: 3.632A  pdb=" N   GLY R 349 " --> pdb=" O   ARG R 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 351 through 361
      removed outlier: 3.615A  pdb=" N   ILE R 355 " --> pdb=" O   PRO R 351 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 361 through 371
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 378 through 385
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.327A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.835A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      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)
    Processing sheet with id=AA2, 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=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.730A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      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: 6.451A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152
      removed outlier: 3.507A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      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=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.764A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.569A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (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=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11
      removed outlier: 5.475A  pdb=" N   GLN N 120 " --> pdb=" O   CYS N  96 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   CYS N  96 " --> pdb=" O   GLN N 120 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   VAL N  48 " --> pdb=" O   TYR N  60 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   TYR N  60 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASP N  50 " --> pdb=" O   ILE N  58 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 180 through 182

    422 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 0.90 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:
        0.00 -     6.80: 11277
        6.80 -    13.59: 64
       13.59 -    20.39: 2
       20.39 -    27.19: 1
       27.19 -    33.99: 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: 2594
        2.84 -     3.35: 7953
        3.35 -     3.87: 13738
        3.87 -     4.38: 16859
        4.38 -     4.90: 27116
  Nonbonded interactions: 68260
  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 3.120
  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 3.040
  ... (remaining 68255 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:8.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.080
-------------------------------------------------------------------------------
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   8384  Z= 1.007
  Angle     :  1.842  33.986  11352  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 : 8.23
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.008   0.001   ARG N  72 
 TYR   0.085   0.009   TYR R 179 
 PHE   0.050   0.006   PHE N  27 
 TRP   0.050   0.011   TRP B  99 
 HIS   0.007   0.003   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.01935 ( 8381)
  covalent geometry    : angle       1.84170 (11346)
  SS BOND              : bond        0.00625 (    3)
  SS BOND              : angle       1.43979 (    6)
  hydrogen bonds       : bond        0.18283 (  422)
  hydrogen bonds       : angle       7.17426 ( 1194)

*********************** 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 to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 ASP cc_start: 0.4362 (p0) cc_final: 0.2844 (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: 0.6362
  time to fit residues: 59.3393
Evaluate side-chains
  60 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
R 207 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.270736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.231686 restraints weight = 8828.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.4570 rms_B_bonded: 2.57
r_work: 0.4448 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0819
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8384  Z= 0.166
  Angle     :  0.726   9.015  11352  Z= 0.388
  Chirality :  0.047   0.216   1282
  Planarity :  0.005   0.072   1440
  Dihedral  :  7.238  82.004   1163
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  6.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.26), residues: 1018
  helix:  1.55 (0.26), residues: 383
  sheet:  1.11 (0.32), residues: 227
  loop : -0.09 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R  73 
 TYR   0.015   0.002   TYR N  95 
 PHE   0.017   0.002   PHE B 278 
 TRP   0.024   0.002   TRP R 326 
 HIS   0.006   0.002   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8381)
  covalent geometry    : angle       0.72539 (11346)
  SS BOND              : bond        0.00400 (    3)
  SS BOND              : angle       1.03416 (    6)
  hydrogen bonds       : bond        0.05382 (  422)
  hydrogen bonds       : angle       5.36291 ( 1194)

*********************** 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
  76 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  188 MET cc_start: 0.2454 (OUTLIER) cc_final: 0.0089 (ttt)
  outliers start: 12
  outliers final: 4
  residues processed: 69
  average time/residue: 0.6094
  time to fit residues: 44.7402
Evaluate side-chains
  52 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  350 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 264 ASN
A 294 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N 123 GLN
R  69 ASN
** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.289852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.253063 restraints weight = 9023.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4721 rms_B_bonded: 2.45
r_work: 0.4618 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2081
moved from start:          0.5986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.115   8384  Z= 0.226
  Angle     :  0.767  11.546  11352  Z= 0.403
  Chirality :  0.046   0.179   1282
  Planarity :  0.006   0.072   1440
  Dihedral  :  7.138  99.477   1157
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  8.06 %
    Favored  : 89.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.26), residues: 1018
  helix:  1.30 (0.26), residues: 402
  sheet:  0.88 (0.33), residues: 235
  loop : -0.26 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.030   0.001   ARG G  13 
 TYR   0.017   0.002   TYR R 176 
 PHE   0.024   0.002   PHE B 234 
 TRP   0.039   0.003   TRP R 166 
 HIS   0.008   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 8381)
  covalent geometry    : angle       0.76658 (11346)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.98180 (    6)
  hydrogen bonds       : bond        0.05123 (  422)
  hydrogen bonds       : angle       5.00782 ( 1194)

*********************** 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
  94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 THR cc_start: 0.2141 (OUTLIER) cc_final: 0.1891 (p)
REVERT: G   21 MET cc_start: 0.3484 (mtm) cc_final: 0.2760 (ptm)
REVERT: R  198 PHE cc_start: 0.4625 (t80) cc_final: 0.4028 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 88
  average time/residue: 0.5380
  time to fit residues: 50.6697
Evaluate side-chains
  63 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
G  44 HIS
R 304 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4995 r_free = 0.4995 target = 0.290949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.254682 restraints weight = 9519.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.4745 rms_B_bonded: 2.48
r_work: 0.4642 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2752
moved from start:          0.7549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8384  Z= 0.163
  Angle     :  0.682   8.116  11352  Z= 0.356
  Chirality :  0.044   0.190   1282
  Planarity :  0.006   0.083   1440
  Dihedral  :  6.494  79.900   1157
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  8.73 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1018
  helix:  1.31 (0.26), residues: 412
  sheet:  0.62 (0.33), residues: 227
  loop : -0.31 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N  72 
 TYR   0.015   0.002   TYR R  48 
 PHE   0.015   0.002   PHE R 198 
 TRP   0.024   0.003   TRP B 211 
 HIS   0.011   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 8381)
  covalent geometry    : angle       0.68163 (11346)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       1.29686 (    6)
  hydrogen bonds       : bond        0.04645 (  422)
  hydrogen bonds       : angle       4.91545 ( 1194)

*********************** 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 to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 LYS cc_start: 0.4908 (mmtp) cc_final: 0.4210 (tptt)
REVERT: G   21 MET cc_start: 0.3221 (mtm) cc_final: 0.2733 (ptm)
REVERT: N   83 MET cc_start: 0.1405 (OUTLIER) cc_final: -0.0345 (mtm)
REVERT: R  121 MET cc_start: 0.4375 (tpt) cc_final: 0.3544 (tpp)
REVERT: R  166 TRP cc_start: 0.6099 (m100) cc_final: 0.4591 (m100)
REVERT: R  226 MET cc_start: 0.6263 (tpp) cc_final: 0.5004 (ttt)
  outliers start: 21
  outliers final: 7
  residues processed: 86
  average time/residue: 0.5007
  time to fit residues: 46.2124
Evaluate side-chains
  61 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue  115 LYS
Chi-restraints excluded: chain R residue  119 TYR
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 230 ASN
B 340 ASN
N  82 GLN
N 123 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5035 r_free = 0.5035 target = 0.297161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.260037 restraints weight = 9737.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.4780 rms_B_bonded: 2.58
r_work: 0.4671 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4033
moved from start:          1.0319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8384  Z= 0.209
  Angle     :  0.732   8.576  11352  Z= 0.385
  Chirality :  0.046   0.279   1282
  Planarity :  0.006   0.089   1440
  Dihedral  :  5.703  58.105   1157
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.53 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.26), residues: 1018
  helix:  1.37 (0.26), residues: 405
  sheet:  0.32 (0.37), residues: 203
  loop : -0.57 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 197 
 TYR   0.017   0.002   TYR R  48 
 PHE   0.024   0.002   PHE G  61 
 TRP   0.050   0.003   TRP B  63 
 HIS   0.007   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 8381)
  covalent geometry    : angle       0.73187 (11346)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       1.38642 (    6)
  hydrogen bonds       : bond        0.05008 (  422)
  hydrogen bonds       : angle       4.97131 ( 1194)

*********************** 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
  111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 ILE cc_start: 0.6725 (mt) cc_final: 0.6492 (mt)
REVERT: B  150 ARG cc_start: 0.4241 (mmt180) cc_final: 0.3823 (mmt90)
REVERT: B  325 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5894 (mmp)
REVERT: N   34 MET cc_start: 0.1117 (ppp) cc_final: 0.0197 (pmm)
REVERT: R  226 MET cc_start: 0.6522 (tpp) cc_final: 0.5861 (ttt)
REVERT: R  373 MET cc_start: 0.6596 (tpp) cc_final: 0.6369 (ttm)
  outliers start: 21
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4353
  time to fit residues: 46.6149
Evaluate side-chains
  82 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   49 ARG
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  118 THR
Chi-restraints excluded: chain R residue  350 THR
Chi-restraints excluded: chain R residue  364 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.289100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.242119 restraints weight = 9505.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.4655 rms_B_bonded: 2.88
r_work: 0.4528 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5727
moved from start:          1.5800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   8384  Z= 0.304
  Angle     :  0.959  12.996  11352  Z= 0.506
  Chirality :  0.054   0.283   1282
  Planarity :  0.007   0.089   1440
  Dihedral  :  6.696  61.669   1155
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.44 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.26), residues: 1018
  helix:  0.42 (0.25), residues: 408
  sheet:  0.08 (0.35), residues: 218
  loop : -1.13 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.049   0.004   TYR B  59 
 PHE   0.029   0.003   PHE N 103 
 TRP   0.039   0.004   TRP B  63 
 HIS   0.012   0.003   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 ( 8381)
  covalent geometry    : angle       0.95840 (11346)
  SS BOND              : bond        0.00107 (    3)
  SS BOND              : angle       1.75416 (    6)
  hydrogen bonds       : bond        0.06939 (  422)
  hydrogen bonds       : angle       5.87203 ( 1194)

*********************** 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
  154 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.4719 (tpp) cc_final: 0.4392 (tmm)
REVERT: B   69 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7259 (mt)
REVERT: G   48 ASP cc_start: 0.7851 (t0) cc_final: 0.7597 (t0)
REVERT: R  195 MET cc_start: 0.4312 (tpp) cc_final: 0.3901 (ttp)
REVERT: R  237 TYR cc_start: 0.6769 (t80) cc_final: 0.6251 (t80)
REVERT: R  372 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6905 (t80)
  outliers start: 24
  outliers final: 8
  residues processed: 147
  average time/residue: 0.3883
  time to fit residues: 62.0804
Evaluate side-chains
  99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  183 VAL
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: 100
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 77 optimal weight:    0.4980
   chunk 81 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 295 ASN
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.286619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.238172 restraints weight = 9523.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.4602 rms_B_bonded: 2.83
r_work: 0.4475 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          1.6335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8384  Z= 0.151
  Angle     :  0.691   7.764  11352  Z= 0.358
  Chirality :  0.045   0.221   1282
  Planarity :  0.005   0.089   1440
  Dihedral  :  5.603  51.207   1155
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.03 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.27), residues: 1018
  helix:  1.31 (0.27), residues: 394
  sheet:  0.16 (0.36), residues: 212
  loop : -0.84 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 231 
 TYR   0.014   0.002   TYR N 115 
 PHE   0.013   0.002   PHE N 103 
 TRP   0.021   0.002   TRP B  99 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8381)
  covalent geometry    : angle       0.69069 (11346)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.11100 (    6)
  hydrogen bonds       : bond        0.04834 (  422)
  hydrogen bonds       : angle       5.00182 ( 1194)

*********************** 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 to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  197 ARG cc_start: 0.7320 (tmm-80) cc_final: 0.6982 (ttp80)
REVERT: B  199 PHE cc_start: 0.3877 (m-10) cc_final: 0.3667 (m-10)
REVERT: G   48 ASP cc_start: 0.8053 (t0) cc_final: 0.7812 (t0)
REVERT: G   61 PHE cc_start: 0.4289 (OUTLIER) cc_final: 0.2974 (t80)
REVERT: R  195 MET cc_start: 0.4584 (tpp) cc_final: 0.4068 (ttm)
REVERT: R  237 TYR cc_start: 0.7010 (t80) cc_final: 0.6502 (t80)
REVERT: R  372 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6889 (t80)
REVERT: R  377 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5815 (t80)
  outliers start: 22
  outliers final: 8
  residues processed: 119
  average time/residue: 0.4261
  time to fit residues: 54.8710
Evaluate side-chains
  100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  183 VAL
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Chi-restraints excluded: chain R residue  377 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0070
   chunk 62 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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**
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  69 ASN
R 207 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.281668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.230756 restraints weight = 9208.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.4556 rms_B_bonded: 2.87
r_work: 0.4429 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5897
moved from start:          1.6847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8384  Z= 0.137
  Angle     :  0.664  12.103  11352  Z= 0.346
  Chirality :  0.044   0.210   1282
  Planarity :  0.005   0.086   1440
  Dihedral  :  5.324  47.280   1155
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.54 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.48 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.27), residues: 1018
  helix:  1.67 (0.27), residues: 393
  sheet:  0.18 (0.37), residues: 224
  loop : -0.74 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.016   0.002   TYR N 115 
 PHE   0.017   0.001   PHE A 238 
 TRP   0.014   0.002   TRP B 297 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8381)
  covalent geometry    : angle       0.66080 (11346)
  SS BOND              : bond        0.00524 (    3)
  SS BOND              : angle       2.91739 (    6)
  hydrogen bonds       : bond        0.04398 (  422)
  hydrogen bonds       : angle       4.67204 ( 1194)

*********************** 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
  118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.3708 (OUTLIER) cc_final: 0.3371 (mp10)
REVERT: B  199 PHE cc_start: 0.4046 (m-10) cc_final: 0.3831 (m-10)
REVERT: B  211 TRP cc_start: 0.2637 (OUTLIER) cc_final: 0.2293 (t60)
REVERT: G   48 ASP cc_start: 0.8221 (t0) cc_final: 0.7960 (t0)
REVERT: G   61 PHE cc_start: 0.4568 (OUTLIER) cc_final: 0.3154 (t80)
REVERT: R  195 MET cc_start: 0.4613 (tpp) cc_final: 0.4063 (ttp)
REVERT: R  237 TYR cc_start: 0.6878 (t80) cc_final: 0.6416 (t80)
REVERT: R  372 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6961 (t80)
  outliers start: 20
  outliers final: 7
  residues processed: 110
  average time/residue: 0.4879
  time to fit residues: 57.4874
Evaluate side-chains
  95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  183 VAL
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: 100
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0030
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.6992

-------------------------------------------------------------------------------
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**
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.278059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.226305 restraints weight = 9189.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4524 rms_B_bonded: 2.90
r_work: 0.4402 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5980
moved from start:          1.7503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8384  Z= 0.135
  Angle     :  0.672  11.717  11352  Z= 0.348
  Chirality :  0.043   0.189   1282
  Planarity :  0.005   0.080   1440
  Dihedral  :  5.305  45.440   1155
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.95 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 20.83 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 1018
  helix:  1.73 (0.27), residues: 394
  sheet:  0.20 (0.36), residues: 229
  loop : -0.69 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG N  98 
 TYR   0.021   0.002   TYR B  85 
 PHE   0.014   0.001   PHE B 235 
 TRP   0.021   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8381)
  covalent geometry    : angle       0.66951 (11346)
  SS BOND              : bond        0.00329 (    3)
  SS BOND              : angle       2.47310 (    6)
  hydrogen bonds       : bond        0.04352 (  422)
  hydrogen bonds       : angle       4.61498 ( 1194)

*********************** 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 to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6911 (mm-30)
REVERT: B  217 MET cc_start: 0.5010 (tpp) cc_final: 0.4069 (ttm)
REVERT: B  262 MET cc_start: 0.4628 (tpp) cc_final: 0.3993 (mmt)
REVERT: B  264 TYR cc_start: 0.8184 (m-80) cc_final: 0.7901 (m-80)
REVERT: G   48 ASP cc_start: 0.8287 (t0) cc_final: 0.8008 (t0)
REVERT: G   61 PHE cc_start: 0.4653 (OUTLIER) cc_final: 0.3173 (t80)
REVERT: R  195 MET cc_start: 0.4840 (tpp) cc_final: 0.4329 (ttm)
REVERT: R  306 MET cc_start: 0.5526 (mmp) cc_final: 0.5206 (mmm)
REVERT: R  372 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7022 (t80)
REVERT: R  379 LEU cc_start: 0.5598 (mp) cc_final: 0.5333 (tp)
  outliers start: 18
  outliers final: 11
  residues processed: 105
  average time/residue: 0.4653
  time to fit residues: 52.6632
Evaluate side-chains
  97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  183 VAL
Chi-restraints excluded: chain R residue  362 SER
Chi-restraints excluded: chain R residue  364 CYS
Chi-restraints excluded: chain R residue  372 PHE
Chi-restraints excluded: chain R residue  377 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4814 r_free = 0.4814 target = 0.263728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.211929 restraints weight = 8937.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.4415 rms_B_bonded: 2.64
r_work: 0.4283 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          1.8646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   8384  Z= 0.154
  Angle     :  0.726  10.519  11352  Z= 0.371
  Chirality :  0.045   0.174   1282
  Planarity :  0.006   0.084   1440
  Dihedral  :  5.460  47.915   1155
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.63 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.84 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.27), residues: 1018
  helix:  1.63 (0.27), residues: 399
  sheet: -0.11 (0.36), residues: 218
  loop : -0.77 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  68 
 TYR   0.017   0.002   TYR N 115 
 PHE   0.021   0.002   PHE B 235 
 TRP   0.023   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8381)
  covalent geometry    : angle       0.72559 (11346)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       1.39266 (    6)
  hydrogen bonds       : bond        0.04626 (  422)
  hydrogen bonds       : angle       4.69031 ( 1194)

********************** 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
  117 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 MET cc_start: 0.1690 (tmt) cc_final: -0.0752 (mmt)
REVERT: B   91 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.6097 (m170)
REVERT: B  168 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6884 (mp)
REVERT: B  217 MET cc_start: 0.6032 (tpp) cc_final: 0.5193 (pp-130)
REVERT: B  262 MET cc_start: 0.5561 (tpp) cc_final: 0.5013 (mmt)
REVERT: G   48 ASP cc_start: 0.8317 (t0) cc_final: 0.8026 (t70)
REVERT: G   61 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.3599 (t80)
REVERT: R  195 MET cc_start: 0.5236 (tpp) cc_final: 0.4790 (mtm)
REVERT: R  306 MET cc_start: 0.5755 (mmp) cc_final: 0.5339 (mmm)
REVERT: R  372 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: R  382 MET cc_start: 0.3828 (mmp) cc_final: 0.3573 (mtt)
  outliers start: 20
  outliers final: 9
  residues processed: 110
  average time/residue: 0.4277
  time to fit residues: 51.2111
Evaluate side-chains
  101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  121 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain G residue   61 PHE
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  183 VAL
Chi-restraints excluded: chain R residue  362 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: 100
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 4 optimal weight:   20.0000
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.263696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.211003 restraints weight = 8972.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.4404 rms_B_bonded: 2.80
r_work: 0.4265 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          1.9428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8384  Z= 0.153
  Angle     :  0.699  11.297  11352  Z= 0.361
  Chirality :  0.044   0.158   1282
  Planarity :  0.005   0.083   1440
  Dihedral  :  5.544  50.115   1155
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.85 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 23.29 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.27), residues: 1018
  helix:  1.48 (0.27), residues: 403
  sheet:  0.03 (0.35), residues: 221
  loop : -0.64 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  68 
 TYR   0.022   0.002   TYR N 115 
 PHE   0.021   0.002   PHE A 273 
 TRP   0.025   0.002   TRP B  63 
 HIS   0.009   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8381)
  covalent geometry    : angle       0.69815 (11346)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       1.80018 (    6)
  hydrogen bonds       : bond        0.04748 (  422)
  hydrogen bonds       : angle       4.69392 ( 1194)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2708.71 seconds
wall clock time: 46 minutes 57.61 seconds (2817.61 seconds total)