Starting phenix.real_space_refine
on Fri Jun  6 19:48:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xov_33360/06_2025/7xov_33360_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xov_33360/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xov_33360/06_2025/7xov_33360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xov_33360/06_2025/7xov_33360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xov_33360/06_2025/7xov_33360_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xov_33360/06_2025/7xov_33360_trim.cif"
  }
  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. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.17, 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  - 3.00
        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: 2.22
  Conformation dependent library (CDL) restraints added in 961.2 milliseconds
  

  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: 0.94
  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: 2.36

  Time building geometry restraints manager: 2.55 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:                         0.000
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.710
  Find NCS groups from input model:        0.080
  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:13.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.830
-------------------------------------------------------------------------------
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 : 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 

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

*********************** 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  : 0.781 
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: 1.2661
  time to fit residues: 118.6697
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  : 0.854 
-------------------------------------------------------------------------------
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 84 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0470
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 78 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 ** 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 = 0.4849 r_free = 0.4849 target = 0.268708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.229436 restraints weight = 8713.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4554 rms_B_bonded: 2.56
r_work: 0.4431 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0677
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8384  Z= 0.162
  Angle     :  0.710   8.248  11352  Z= 0.383
  Chirality :  0.046   0.195   1282
  Planarity :  0.005   0.078   1440
  Dihedral  :  7.085  77.682   1163
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.16 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.61 %
    Favored  : 92.39 %
  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:  1.31 (0.26), residues: 1018
  helix:  1.67 (0.26), residues: 387
  sheet:  1.23 (0.32), residues: 225
  loop : -0.05 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 326 
 HIS   0.006   0.002   HIS B 225 
 PHE   0.019   0.002   PHE B 278 
 TYR   0.015   0.002   TYR N  95 
 ARG   0.006   0.001   ARG R  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05571 (  422)
  hydrogen bonds       : angle       5.33339 ( 1194)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       1.02710 (    6)
  covalent geometry    : bond        0.00326 ( 8381)
  covalent geometry    : angle       0.70936 (11346)

*********************** 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
  72 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: B  188 MET cc_start: 0.2434 (OUTLIER) cc_final: 0.0001 (ttt)
REVERT: G   21 MET cc_start: 0.3750 (mtm) cc_final: 0.3485 (ttt)
REVERT: R   72 MET cc_start: 0.1356 (mmt) cc_final: 0.0583 (mpp)
  outliers start: 9
  outliers final: 4
  residues processed: 66
  average time/residue: 1.4634
  time to fit residues: 103.1284
Evaluate side-chains
  55 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  336 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 86 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 176 GLN
B 230 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
N  35 ASN
N  82 GLN
** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 ASN
R 207 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5119 r_free = 0.5119 target = 0.310053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4915 r_free = 0.4915 target = 0.276027 restraints weight = 10047.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.4902 rms_B_bonded: 2.64
r_work: 0.4803 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4370
moved from start:          1.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.290   8384  Z= 0.480
  Angle     :  1.349  26.350  11352  Z= 0.716
  Chirality :  0.066   0.289   1282
  Planarity :  0.011   0.101   1440
  Dihedral  : 10.582 120.101   1161
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 22.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  6.38 %
    Favored  : 90.37 %
  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: -1.50 (0.24), residues: 1018
  helix: -0.85 (0.23), residues: 405
  sheet: -0.56 (0.34), residues: 218
  loop : -1.20 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.005   TRP R 166 
 HIS   0.022   0.004   HIS A  41 
 PHE   0.040   0.005   PHE N 108 
 TYR   0.041   0.005   TYR N  80 
 ARG   0.054   0.002   ARG R  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09108 (  422)
  hydrogen bonds       : angle       7.09312 ( 1194)
  SS BOND              : bond        0.00585 (    3)
  SS BOND              : angle       4.04740 (    6)
  covalent geometry    : bond        0.01014 ( 8381)
  covalent geometry    : angle       1.34646 (11346)

*********************** 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
  152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.3470 (OUTLIER) cc_final: 0.1850 (mp10)
REVERT: A  386 MET cc_start: 0.6240 (mpp) cc_final: 0.6020 (mtm)
REVERT: B  323 ASP cc_start: 0.6114 (p0) cc_final: 0.5849 (p0)
REVERT: R  195 MET cc_start: 0.3519 (tpt) cc_final: 0.2974 (ptm)
REVERT: R  327 MET cc_start: 0.3427 (OUTLIER) cc_final: 0.3200 (mtm)
  outliers start: 29
  outliers final: 4
  residues processed: 140
  average time/residue: 0.9606
  time to fit residues: 145.2849
Evaluate side-chains
  85 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain A residue  357 HIS
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain R residue  327 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5069 r_free = 0.5069 target = 0.301270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.263216 restraints weight = 9863.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.4794 rms_B_bonded: 2.74
r_work: 0.4686 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4630
moved from start:          1.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8384  Z= 0.173
  Angle     :  0.748   9.791  11352  Z= 0.389
  Chirality :  0.045   0.173   1282
  Planarity :  0.006   0.075   1440
  Dihedral  :  6.715  73.775   1155
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.21 %
    Favored  : 83.99 %
  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: -0.37 (0.26), residues: 1018
  helix:  0.49 (0.26), residues: 408
  sheet: -0.18 (0.32), residues: 231
  loop : -0.97 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP B 169 
 HIS   0.004   0.001   HIS A  41 
 PHE   0.016   0.002   PHE B 234 
 TYR   0.018   0.002   TYR R 119 
 ARG   0.006   0.001   ARG R  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05160 (  422)
  hydrogen bonds       : angle       5.52758 ( 1194)
  SS BOND              : bond        0.00132 (    3)
  SS BOND              : angle       0.79405 (    6)
  covalent geometry    : bond        0.00371 ( 8381)
  covalent geometry    : angle       0.74814 (11346)

*********************** 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
  113 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLN cc_start: 0.3302 (OUTLIER) cc_final: 0.2202 (mp10)
REVERT: N   83 MET cc_start: 0.2469 (OUTLIER) cc_final: 0.0876 (mpp)
REVERT: R  195 MET cc_start: 0.3435 (tpt) cc_final: 0.2942 (mtp)
  outliers start: 25
  outliers final: 6
  residues processed: 105
  average time/residue: 0.9135
  time to fit residues: 104.2597
Evaluate side-chains
  74 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   63 ILE
Chi-restraints excluded: chain R residue  136 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0000
   chunk 68 optimal weight:    0.0070
   chunk 66 optimal weight:    0.0170
   chunk 69 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.3040

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 123 GLN
R  69 ASN
R 207 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5048 r_free = 0.5048 target = 0.298513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.259462 restraints weight = 9708.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.4768 rms_B_bonded: 2.77
r_work: 0.4656 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.4656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4697
moved from start:          1.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8384  Z= 0.129
  Angle     :  0.675   9.277  11352  Z= 0.344
  Chirality :  0.044   0.168   1282
  Planarity :  0.005   0.081   1440
  Dihedral  :  5.994  62.169   1155
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.45 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.27), residues: 1018
  helix:  1.15 (0.26), residues: 407
  sheet:  0.05 (0.34), residues: 225
  loop : -0.73 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.014   0.001   PHE G  61 
 TYR   0.015   0.002   TYR B  85 
 ARG   0.007   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  422)
  hydrogen bonds       : angle       4.94971 ( 1194)
  SS BOND              : bond        0.00121 (    3)
  SS BOND              : angle       0.93086 (    6)
  covalent geometry    : bond        0.00261 ( 8381)
  covalent geometry    : angle       0.67470 (11346)

*********************** 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
  100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.5124 (mttt) cc_final: 0.4840 (tppt)
REVERT: A  227 GLN cc_start: 0.3297 (OUTLIER) cc_final: 0.2740 (mp10)
REVERT: B  188 MET cc_start: 0.6840 (mpt) cc_final: 0.6602 (mmt)
REVERT: R  195 MET cc_start: 0.3161 (tpt) cc_final: 0.2706 (mtp)
REVERT: R  372 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6860 (t80)
  outliers start: 20
  outliers final: 7
  residues processed: 90
  average time/residue: 0.9944
  time to fit residues: 97.0139
Evaluate side-chains
  76 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  227 GLN
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  372 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
N 123 GLN
** R  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 ASN
R 207 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4943 r_free = 0.4943 target = 0.283148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.233529 restraints weight = 9361.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.4593 rms_B_bonded: 2.91
r_work: 0.4477 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5828
moved from start:          1.6288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8384  Z= 0.242
  Angle     :  0.900  13.538  11352  Z= 0.465
  Chirality :  0.050   0.264   1282
  Planarity :  0.006   0.087   1440
  Dihedral  :  6.363  49.300   1155
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.56 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.40 (0.26), residues: 1018
  helix:  0.56 (0.25), residues: 409
  sheet: -0.24 (0.35), residues: 213
  loop : -1.05 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP B  63 
 HIS   0.009   0.002   HIS A  41 
 PHE   0.025   0.003   PHE N 103 
 TYR   0.020   0.003   TYR R 179 
 ARG   0.011   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06544 (  422)
  hydrogen bonds       : angle       5.51555 ( 1194)
  SS BOND              : bond        0.00326 (    3)
  SS BOND              : angle       1.53092 (    6)
  covalent geometry    : bond        0.00536 ( 8381)
  covalent geometry    : angle       0.89966 (11346)

*********************** 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
  149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6858 (mm-30)
REVERT: A  227 GLN cc_start: 0.4054 (OUTLIER) cc_final: 0.3445 (mp10)
REVERT: A  389 ARG cc_start: 0.7433 (mtt180) cc_final: 0.7204 (mmt-90)
REVERT: B   69 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7417 (mt)
REVERT: B  211 TRP cc_start: 0.3117 (OUTLIER) cc_final: 0.2362 (t60)
REVERT: N   83 MET cc_start: 0.4133 (ppp) cc_final: 0.1868 (mmp)
REVERT: R  137 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7824 (mt)
REVERT: R  195 MET cc_start: 0.4561 (tpt) cc_final: 0.4324 (ptp)
REVERT: R  237 TYR cc_start: 0.6782 (t80) cc_final: 0.6242 (t80)
REVERT: R  372 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7154 (t80)
  outliers start: 32
  outliers final: 2
  residues processed: 138
  average time/residue: 0.8682
  time to fit residues: 129.9611
Evaluate side-chains
  95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  137 LEU
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 83 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0570
   chunk 82 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 206 GLN
R 207 GLN
R 210 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.276395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.226697 restraints weight = 9116.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.4526 rms_B_bonded: 2.76
r_work: 0.4401 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5888
moved from start:          1.6737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8384  Z= 0.148
  Angle     :  0.705   8.882  11352  Z= 0.366
  Chirality :  0.045   0.221   1282
  Planarity :  0.005   0.063   1440
  Dihedral  :  5.663  47.573   1155
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.58 %
    Favored  : 80.18 %
  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:  0.35 (0.27), residues: 1018
  helix:  1.37 (0.27), residues: 406
  sheet: -0.18 (0.34), residues: 236
  loop : -0.65 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  99 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.045   0.002   PHE G  61 
 TYR   0.017   0.002   TYR B  85 
 ARG   0.011   0.001   ARG R 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04624 (  422)
  hydrogen bonds       : angle       4.89420 ( 1194)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       2.34085 (    6)
  covalent geometry    : bond        0.00318 ( 8381)
  covalent geometry    : angle       0.70290 (11346)

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

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.3961 (m100) cc_final: 0.3751 (m100)
REVERT: B  197 ARG cc_start: 0.6925 (tmm-80) cc_final: 0.6436 (ttp80)
REVERT: B  199 PHE cc_start: 0.4207 (m-10) cc_final: 0.3970 (m-10)
REVERT: B  211 TRP cc_start: 0.3198 (OUTLIER) cc_final: 0.2922 (t60)
REVERT: N   83 MET cc_start: 0.4327 (OUTLIER) cc_final: 0.1882 (mmp)
REVERT: R  137 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7831 (mt)
REVERT: R  195 MET cc_start: 0.4504 (tpt) cc_final: 0.4259 (ptp)
REVERT: R  237 TYR cc_start: 0.6886 (t80) cc_final: 0.6416 (t80)
REVERT: R  372 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7454 (m-80)
REVERT: R  377 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5631 (m-80)
  outliers start: 20
  outliers final: 5
  residues processed: 108
  average time/residue: 1.0500
  time to fit residues: 123.4081
Evaluate side-chains
  92 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue  137 LEU
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 33 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 56 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** 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 = 0.4862 r_free = 0.4862 target = 0.271670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.219253 restraints weight = 9196.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.4479 rms_B_bonded: 2.84
r_work: 0.4359 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6166
moved from start:          1.8067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8384  Z= 0.185
  Angle     :  0.733   8.977  11352  Z= 0.384
  Chirality :  0.046   0.181   1282
  Planarity :  0.005   0.053   1440
  Dihedral  :  5.746  50.574   1155
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.93 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.04 %
    Favored  : 78.50 %
  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:  0.49 (0.27), residues: 1018
  helix:  1.53 (0.27), residues: 397
  sheet: -0.13 (0.34), residues: 236
  loop : -0.56 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 339 
 HIS   0.015   0.002   HIS B  54 
 PHE   0.033   0.002   PHE G  61 
 TYR   0.015   0.002   TYR B 264 
 ARG   0.015   0.001   ARG N  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04977 (  422)
  hydrogen bonds       : angle       4.83165 ( 1194)
  SS BOND              : bond        0.00424 (    3)
  SS BOND              : angle       2.36733 (    6)
  covalent geometry    : bond        0.00385 ( 8381)
  covalent geometry    : angle       0.73166 (11346)

*********************** 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
  124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: A  277 TRP cc_start: 0.3461 (t-100) cc_final: 0.3062 (m-90)
REVERT: B   99 TRP cc_start: 0.6174 (m100) cc_final: 0.5899 (t-100)
REVERT: B  228 ASP cc_start: 0.7914 (m-30) cc_final: 0.7603 (m-30)
REVERT: R  137 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7755 (mt)
REVERT: R  225 MET cc_start: 0.7739 (ttt) cc_final: 0.7471 (ttp)
REVERT: R  306 MET cc_start: 0.5812 (mmp) cc_final: 0.5442 (mmm)
  outliers start: 22
  outliers final: 9
  residues processed: 115
  average time/residue: 0.9064
  time to fit residues: 113.9869
Evaluate side-chains
  93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
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  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  136 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  183 VAL
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 25 optimal weight:    7.9990
   chunk 80 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0270
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.272733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.220652 restraints weight = 9272.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.4484 rms_B_bonded: 2.83
r_work: 0.4368 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6138
moved from start:          1.8405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8384  Z= 0.132
  Angle     :  0.665   8.430  11352  Z= 0.347
  Chirality :  0.044   0.226   1282
  Planarity :  0.004   0.045   1440
  Dihedral  :  5.503  46.725   1155
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.34 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 21.95 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1018
  helix:  1.77 (0.27), residues: 397
  sheet: -0.15 (0.33), residues: 236
  loop : -0.48 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.029   0.002   PHE G  61 
 TYR   0.025   0.002   TYR A 391 
 ARG   0.009   0.000   ARG R 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  422)
  hydrogen bonds       : angle       4.59743 ( 1194)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.51205 (    6)
  covalent geometry    : bond        0.00282 ( 8381)
  covalent geometry    : angle       0.66391 (11346)

*********************** 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
  101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.7607 (m-30) cc_final: 0.7354 (m-30)
REVERT: B  262 MET cc_start: 0.5173 (tpp) cc_final: 0.4679 (tpt)
REVERT: R  137 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: R  306 MET cc_start: 0.5743 (mmp) cc_final: 0.5415 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 96
  average time/residue: 1.0151
  time to fit residues: 106.3681
Evaluate side-chains
  94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  136 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  183 VAL
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 0 optimal weight:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0770
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4837 r_free = 0.4837 target = 0.268091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.215692 restraints weight = 9086.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.4452 rms_B_bonded: 2.81
r_work: 0.4334 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6228
moved from start:          1.8769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8384  Z= 0.141
  Angle     :  0.681   8.287  11352  Z= 0.356
  Chirality :  0.045   0.207   1282
  Planarity :  0.004   0.042   1440
  Dihedral  :  5.484  46.603   1155
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.63 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 22.17 %
    Favored  : 76.04 %
  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:  0.75 (0.27), residues: 1018
  helix:  1.81 (0.27), residues: 397
  sheet:  0.04 (0.34), residues: 236
  loop : -0.53 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 277 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.028   0.002   PHE G  61 
 TYR   0.013   0.002   TYR N  60 
 ARG   0.009   0.000   ARG R 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04429 (  422)
  hydrogen bonds       : angle       4.61635 ( 1194)
  SS BOND              : bond        0.00235 (    3)
  SS BOND              : angle       1.50148 (    6)
  covalent geometry    : bond        0.00313 ( 8381)
  covalent geometry    : angle       0.68057 (11346)

********************** 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
  108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  285 THR cc_start: 0.7760 (t) cc_final: 0.7538 (m)
REVERT: B  228 ASP cc_start: 0.7551 (m-30) cc_final: 0.7236 (m-30)
REVERT: B  262 MET cc_start: 0.5909 (tpp) cc_final: 0.5334 (tpt)
REVERT: R  137 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7702 (mt)
REVERT: R  235 GLU cc_start: 0.6620 (tp30) cc_final: 0.6357 (mp0)
REVERT: R  306 MET cc_start: 0.5912 (mmp) cc_final: 0.5498 (mmm)
REVERT: R  372 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7086 (t80)
REVERT: R  379 LEU cc_start: 0.5244 (mp) cc_final: 0.4989 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 103
  average time/residue: 0.8989
  time to fit residues: 100.6267
Evaluate side-chains
  95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  136 SER
Chi-restraints excluded: chain R residue  137 LEU
Chi-restraints excluded: chain R residue  183 VAL
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 0 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 89 optimal weight:    0.5980
   chunk 86 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0370
   chunk 23 optimal weight:   10.0000
   overall best weight:    3.3062

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS
B   6 GLN
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
N  74 ASN
R 206 GLN
R 210 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.242435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.189562 restraints weight = 9050.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 2.75
r_work: 0.4005 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          2.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085   8384  Z= 0.317
  Angle     :  1.010   9.984  11352  Z= 0.540
  Chirality :  0.058   0.303   1282
  Planarity :  0.007   0.065   1440
  Dihedral  :  7.340  60.034   1155
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.81 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 22.28 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.30 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.39 (0.26), residues: 1018
  helix:  0.60 (0.26), residues: 391
  sheet:  0.33 (0.36), residues: 202
  loop : -1.34 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.089   0.006   TRP A 277 
 HIS   0.009   0.002   HIS A 220 
 PHE   0.049   0.004   PHE G  61 
 TYR   0.031   0.004   TYR N 115 
 ARG   0.020   0.001   ARG A 356 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08097 (  422)
  hydrogen bonds       : angle       5.76654 ( 1194)
  SS BOND              : bond        0.00597 (    3)
  SS BOND              : angle       2.53892 (    6)
  covalent geometry    : bond        0.00744 ( 8381)
  covalent geometry    : angle       1.00906 (11346)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5971.38 seconds
wall clock time: 104 minutes 28.35 seconds (6268.35 seconds total)