Starting phenix.real_space_refine
on Thu Mar 13 16:52:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxd_24729/03_2025/7rxd_24729.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    5749      2.51       5
     N    1490      2.21       5
     O    1737      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9007
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3433
          Classifications: {'peptide': 439}
          Link IDs: {'PTRANS': 24, 'TRANS': 414}
          Chain breaks: 4
    Chain: "H"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1582
          Classifications: {'peptide': 207}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 204, 1588
          Classifications: {'peptide': 204}
          Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 990
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 173, 1391
          Classifications: {'peptide': 173}
          Link IDs: {'PTRANS': 9, 'TRANS': 163}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.42, per 1000 atoms: 0.60
  Number of scatterers: 9007
  At special positions: 0
  Unit cell: (118.72, 133.56, 111.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1737      8.00
     N    1490      7.00
     C    5749      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 150 " - pdb=" SG  CYS H 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 139 " - pdb=" SG  CYS L 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03

  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
  Links applied
    ALPHA1-4
      " GLC A   1 " - " GLC A   2 "
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 953.7 milliseconds
  

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 22 sheets defined
      27.9% alpha, 33.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 28
    Processing helix  chain 'B' and resid 43 through 52
      Proline residue:  B  49  - end of helix
    Processing helix  chain 'B' and resid 64 through 74
      removed outlier: 4.055A  pdb=" N   PHE B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY B  69 " --> pdb=" O   HIS B  65 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLY B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 89
    Processing helix  chain 'B' and resid 91 through 98
      removed outlier: 3.553A  pdb=" N   TRP B  95 " --> pdb=" O   TYR B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 141
      removed outlier: 4.490A  pdb=" N   ALA B 135 " --> pdb=" O   GLU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 164
      removed outlier: 3.923A  pdb=" N   THR B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
    Processing helix  chain 'B' and resid 182 through 185
      removed outlier: 4.399A  pdb=" N   ASP B 185 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 182 through 185'
    Processing helix  chain 'B' and resid 186 through 202
    Processing helix  chain 'B' and resid 210 through 220
    Processing helix  chain 'B' and resid 229 through 231
      No H-bonds generated for 'chain 'B' and resid 229 through 231'
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 287 through 298
      removed outlier: 3.640A  pdb=" N   ASP B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 313
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 336 through 353
      removed outlier: 3.913A  pdb=" N   PHE B 340 " --> pdb=" O   GLN B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 370
      removed outlier: 3.610A  pdb=" N   MET B 370 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 388
    Processing helix  chain 'B' and resid 391 through 406
    Processing helix  chain 'B' and resid 502 through 517
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.568A  pdb=" N   PHE H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.798A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
    Processing helix  chain 'L' and resid 126 through 133
    Processing helix  chain 'L' and resid 188 through 194
      removed outlier: 3.722A  pdb=" N   HIS L 194 " --> pdb=" O   ASP L 190 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.531A  pdb=" N   LYS N  65 " --> pdb=" O   ASP N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 337 through 343
      removed outlier: 3.748A  pdb=" N   VAL R 341 " --> pdb=" O   PRO R 337 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 365 through 370
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.798A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 410
      removed outlier: 4.935A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'R' and resid 438 through 443
    Processing helix  chain 'R' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.958A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ALA B 265 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39
      removed outlier: 5.958A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  39 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL B   9 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   PHE B  62 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP B  11 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100
    Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228
    Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173
      removed outlier: 4.055A  pdb=" N   LYS B 171 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.770A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA H  40 " --> pdb=" O   GLY H  44 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.043A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134
      removed outlier: 4.043A  pdb=" N   GLY H 149 " --> pdb=" O   LEU H 134 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.835A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.835A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.682A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154
    Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.299A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER N 120 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 120 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   LYS N  99 " --> pdb=" O   ARG N  33 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ARG N  33 " --> pdb=" O   LYS N  99 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   MET N  34 " --> pdb=" O   ALA N  50 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.299A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER N 120 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 120 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.921A  pdb=" N   VAL R 395 " --> pdb=" O   ILE R 358 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474

    423 hydrogen bonds defined for protein.
    1116 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: 2.99

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2864
        1.35 -     1.48: 2471
        1.48 -     1.61: 3844
        1.61 -     1.74: 0
        1.74 -     1.87: 47
  Bond restraints: 9226
  Sorted by residual:
  bond pdb=" CB  CYS R 379 "
       pdb=" SG  CYS R 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.875 -0.067 3.30e-02 9.18e+02 4.09e+00
  bond pdb=" CB  VAL N  48 "
       pdb=" CG2 VAL N  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  bond pdb=" CB  CYS R 432 "
       pdb=" SG  CYS R 432 "
    ideal  model  delta    sigma   weight residual
    1.808  1.768  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" C1  GLC A   1 "
       pdb=" O1  GLC A   1 "
    ideal  model  delta    sigma   weight residual
    1.389  1.409 -0.020 2.00e-02 2.50e+03 9.63e-01
  bond pdb=" C   ILE B 133 "
       pdb=" N   PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 9.00e-01
  ... (remaining 9221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 12431
        2.65 -     5.31: 91
        5.31 -     7.96: 3
        7.96 -    10.62: 0
       10.62 -    13.27: 2
  Bond angle restraints: 12527
  Sorted by residual:
  angle pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
        pdb=" C   CYS R 432 "
      ideal   model   delta    sigma   weight residual
     107.88  119.63  -11.75 1.41e+00 5.03e-01 6.95e+01
  angle pdb=" CA  CYS R 432 "
        pdb=" CB  CYS R 432 "
        pdb=" SG  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     114.40  127.67  -13.27 2.30e+00 1.89e-01 3.33e+01
  angle pdb=" C   GLY R 431 "
        pdb=" N   CYS R 432 "
        pdb=" CA  CYS R 432 "
      ideal   model   delta    sigma   weight residual
     122.45  118.44    4.01 1.78e+00 3.16e-01 5.07e+00
  angle pdb=" N   GLU B  23 "
        pdb=" CA  GLU B  23 "
        pdb=" CB  GLU B  23 "
      ideal   model   delta    sigma   weight residual
     110.16  113.37   -3.21 1.48e+00 4.57e-01 4.70e+00
  angle pdb=" C   GLU B 173 "
        pdb=" N   ASN B 174 "
        pdb=" CA  ASN B 174 "
      ideal   model   delta    sigma   weight residual
     121.54  125.58   -4.04 1.91e+00 2.74e-01 4.47e+00
  ... (remaining 12522 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4970
       17.94 -    35.87: 423
       35.87 -    53.81: 73
       53.81 -    71.75: 14
       71.75 -    89.68: 11
  Dihedral angle restraints: 5491
    sinusoidal: 2164
      harmonic: 3327
  Sorted by residual:
  dihedral pdb=" CA  GLU H 158 "
           pdb=" C   GLU H 158 "
           pdb=" N   PRO H 159 "
           pdb=" CA  PRO H 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.49   35.51     0      5.00e+00 4.00e-02 5.04e+01
  dihedral pdb=" CB  CYS R 379 "
           pdb=" SG  CYS R 379 "
           pdb=" SG  CYS R 432 "
           pdb=" CB  CYS R 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.17   58.83     1      1.00e+01 1.00e-02 4.63e+01
  dihedral pdb=" CB  CYS H 150 "
           pdb=" SG  CYS H 150 "
           pdb=" SG  CYS H 206 "
           pdb=" CB  CYS H 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  140.09  -47.09     1      1.00e+01 1.00e-02 3.06e+01
  ... (remaining 5488 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1180
       0.061 -    0.121: 177
       0.121 -    0.182: 8
       0.182 -    0.242: 0
       0.242 -    0.303: 2
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" C1  GLC A   2 "
            pdb=" O4  GLC A   1 "
            pdb=" C2  GLC A   2 "
            pdb=" O5  GLC A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.32    0.08 2.00e-02 2.50e+03 1.72e+01
  chirality pdb=" C1  GLC A   1 "
            pdb=" C2  GLC A   1 "
            pdb=" O1  GLC A   1 "
            pdb=" O5  GLC A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.34    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  CYS R 432 "
            pdb=" N   CYS R 432 "
            pdb=" C   CYS R 432 "
            pdb=" CB  CYS R 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 158 "    0.076 5.00e-02 4.00e+02   1.17e-01 2.19e+01
        pdb=" N   PRO H 159 "   -0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO H 159 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO H 159 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER R 383 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO R 384 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO R 384 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO R 384 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 123 "    0.050 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO B 124 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B 124 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 124 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 200
        2.69 -     3.24: 8625
        3.24 -     3.80: 14199
        3.80 -     4.35: 18927
        4.35 -     4.90: 31721
  Nonbonded interactions: 73672
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R 442 "
            pdb=" OH  TYR R 451 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" O   MET H 110 "
            pdb=" OH  TYR L  42 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" ND2 ASN H 207 "
            pdb=" OD1 ASP H 218 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" OE1 GLN L  27 "
            pdb=" OG1 THR N 118 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OD2 ASP R 398 "
            pdb=" OH  TYR R 423 "
     model   vdw
     2.208 3.040
  ... (remaining 73667 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 group one per residue
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:             0.860
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.530
  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:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
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      :  0.003   0.067   9226  Z= 0.204
  Angle     :  0.575  13.271  12527  Z= 0.302
  Chirality :  0.043   0.303   1367
  Planarity :  0.005   0.117   1604
  Dihedral  : 13.839  89.685   3344
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.21 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.47 (0.25), residues: 1118
  helix:  0.60 (0.33), residues: 261
  sheet:  0.60 (0.27), residues: 346
  loop :  0.11 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L  56 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.020   0.002   PHE B 259 
 TYR   0.015   0.001   TYR R 505 
 ARG   0.003   0.000   ARG N  38 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 1.381 
Fit side-chains
REVERT: B  405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170)
REVERT: B  485 LEU cc_start: 0.8913 (tp) cc_final: 0.8315 (tp)
REVERT: H    6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0)
REVERT: H  153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp)
  outliers start: 2
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2091
  time to fit residues: 42.3548
Evaluate side-chains
  111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.2980
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 204 HIS
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 143 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.206259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.173464 restraints weight = 11861.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176314 restraints weight = 17636.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177430 restraints weight = 12031.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   9226  Z= 0.196
  Angle     :  0.556  14.318  12527  Z= 0.290
  Chirality :  0.042   0.160   1367
  Planarity :  0.005   0.100   1604
  Dihedral  :  4.400  33.374   1277
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.35 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.73 (0.25), residues: 1118
  helix:  1.11 (0.32), residues: 264
  sheet:  0.67 (0.27), residues: 343
  loop :  0.15 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.023   0.001   PHE B 510 
 TYR   0.034   0.001   TYR R 505 
 ARG   0.005   0.001   ARG L 147 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 HIS cc_start: 0.8592 (t-90) cc_final: 0.8094 (t-170)
REVERT: B  485 LEU cc_start: 0.8830 (tp) cc_final: 0.8418 (tp)
REVERT: B  532 PHE cc_start: 0.7622 (m-80) cc_final: 0.7284 (m-80)
REVERT: H    6 GLU cc_start: 0.7160 (mp0) cc_final: 0.6845 (mp0)
REVERT: H  219 LYS cc_start: 0.7403 (tppt) cc_final: 0.7149 (tppt)
  outliers start: 8
  outliers final: 6
  residues processed: 141
  average time/residue: 0.2192
  time to fit residues: 44.7573
Evaluate side-chains
  124 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 204 HIS
L  32 ASN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.203818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.164153 restraints weight = 12108.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.165130 restraints weight = 12200.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.160086 restraints weight = 8483.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9226  Z= 0.223
  Angle     :  0.538  13.399  12527  Z= 0.281
  Chirality :  0.041   0.132   1367
  Planarity :  0.004   0.089   1604
  Dihedral  :  4.320  31.438   1277
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.87 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.81 (0.25), residues: 1118
  helix:  1.24 (0.32), residues: 265
  sheet:  0.67 (0.27), residues: 358
  loop :  0.18 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.032   0.002   PHE B 510 
 TYR   0.024   0.001   TYR R 505 
 ARG   0.003   0.000   ARG L 147 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 HIS cc_start: 0.8631 (t-90) cc_final: 0.8206 (t-170)
REVERT: B  532 PHE cc_start: 0.7924 (m-80) cc_final: 0.7486 (m-80)
REVERT: H    6 GLU cc_start: 0.7086 (mp0) cc_final: 0.6783 (mp0)
REVERT: H  219 LYS cc_start: 0.7527 (tppt) cc_final: 0.7237 (tppt)
REVERT: R  357 ARG cc_start: 0.6869 (ttp-170) cc_final: 0.6623 (ttp-170)
  outliers start: 12
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2052
  time to fit residues: 41.2314
Evaluate side-chains
  135 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   66 ASP
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
B 204 HIS
B 324 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 171 GLN
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135742 restraints weight = 11295.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136102 restraints weight = 16432.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.135712 restraints weight = 11622.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.097   9226  Z= 0.502
  Angle     :  0.699  12.693  12527  Z= 0.365
  Chirality :  0.046   0.250   1367
  Planarity :  0.005   0.083   1604
  Dihedral  :  5.057  30.523   1277
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.39 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.38 (0.25), residues: 1118
  helix:  1.18 (0.33), residues: 254
  sheet:  0.49 (0.27), residues: 351
  loop : -0.31 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP N  47 
 HIS   0.003   0.001   HIS N 124 
 PHE   0.021   0.002   PHE B 259 
 TYR   0.032   0.003   TYR L  97 
 ARG   0.004   0.001   ARG L 147 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  532 PHE cc_start: 0.7616 (m-80) cc_final: 0.6938 (m-80)
REVERT: L  147 ARG cc_start: 0.7318 (ttm110) cc_final: 0.7046 (mtp180)
REVERT: R  357 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.6414 (ttp-170)
  outliers start: 23
  outliers final: 16
  residues processed: 143
  average time/residue: 0.1959
  time to fit residues: 39.6944
Evaluate side-chains
  131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   66 ASP
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   89 GLU
Chi-restraints excluded: chain R residue  392 PHE
Chi-restraints excluded: chain R residue  401 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 98 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 96 optimal weight:    0.3980
   chunk 111 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** R 422 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 = 0.4096 r_free = 0.4096 target = 0.175657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143519 restraints weight = 11154.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139708 restraints weight = 13947.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.135732 restraints weight = 13476.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9226  Z= 0.237
  Angle     :  0.569  13.776  12527  Z= 0.297
  Chirality :  0.042   0.155   1367
  Planarity :  0.004   0.063   1604
  Dihedral  :  4.671  32.024   1277
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.25 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.48 (0.25), residues: 1118
  helix:  1.32 (0.33), residues: 259
  sheet:  0.40 (0.27), residues: 349
  loop : -0.16 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.023   0.001   PHE B 532 
 TYR   0.019   0.001   TYR R 505 
 ARG   0.003   0.000   ARG N  38 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7106 (mm)
REVERT: L   69 THR cc_start: 0.8089 (t) cc_final: 0.7880 (p)
REVERT: L  147 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6970 (mtp180)
REVERT: R  357 ARG cc_start: 0.6684 (ttp-170) cc_final: 0.6412 (ttp-170)
  outliers start: 20
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2210
  time to fit residues: 43.4741
Evaluate side-chains
  134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 1.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  166 SER
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0170
   chunk 110 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
** R 422 ASN ** 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 = 0.4100 r_free = 0.4100 target = 0.175947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.143801 restraints weight = 11194.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140061 restraints weight = 13798.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.138422 restraints weight = 14035.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9226  Z= 0.220
  Angle     :  0.562  13.631  12527  Z= 0.290
  Chirality :  0.042   0.144   1367
  Planarity :  0.004   0.058   1604
  Dihedral  :  4.522  31.373   1277
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.77 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.54 (0.25), residues: 1118
  helix:  1.42 (0.33), residues: 259
  sheet:  0.40 (0.27), residues: 354
  loop : -0.13 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP N  47 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.019   0.001   PHE B 532 
 TYR   0.018   0.001   TYR B 100 
 ARG   0.002   0.000   ARG R 457 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7095 (mm)
REVERT: B  485 LEU cc_start: 0.8850 (tp) cc_final: 0.8589 (tp)
REVERT: L   69 THR cc_start: 0.8068 (t) cc_final: 0.7849 (p)
REVERT: L  147 ARG cc_start: 0.7197 (ttm110) cc_final: 0.6979 (mtp180)
REVERT: R  357 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.6482 (ttp-170)
  outliers start: 21
  outliers final: 15
  residues processed: 143
  average time/residue: 0.2005
  time to fit residues: 40.8849
Evaluate side-chains
  137 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 71 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0040
   chunk 56 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 366 GLN
** R 422 ASN ** 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 = 0.4096 r_free = 0.4096 target = 0.175032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.143549 restraints weight = 11303.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.139050 restraints weight = 13834.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.136515 restraints weight = 13595.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9226  Z= 0.229
  Angle     :  0.570  13.528  12527  Z= 0.295
  Chirality :  0.042   0.144   1367
  Planarity :  0.004   0.050   1604
  Dihedral  :  4.491  31.304   1277
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.77 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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 (0.25), residues: 1118
  helix:  1.40 (0.33), residues: 259
  sheet:  0.40 (0.27), residues: 354
  loop : -0.19 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.001   PHE B 532 
 TYR   0.018   0.001   TYR B 100 
 ARG   0.002   0.000   ARG R 457 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: B   90 LEU cc_start: 0.7787 (mt) cc_final: 0.7356 (mt)
REVERT: B  291 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7066 (mm)
REVERT: L   69 THR cc_start: 0.8004 (t) cc_final: 0.7731 (p)
REVERT: L  147 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6965 (mtp180)
REVERT: R  481 ASN cc_start: 0.6847 (t0) cc_final: 0.6581 (t0)
  outliers start: 28
  outliers final: 22
  residues processed: 141
  average time/residue: 0.2016
  time to fit residues: 40.5676
Evaluate side-chains
  141 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 86 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0000
   chunk 41 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
** R 422 ASN ** 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 = 0.4104 r_free = 0.4104 target = 0.175908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142933 restraints weight = 11318.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.140108 restraints weight = 13532.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.136422 restraints weight = 11609.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   9226  Z= 0.211
  Angle     :  0.569  13.387  12527  Z= 0.291
  Chirality :  0.042   0.147   1367
  Planarity :  0.004   0.051   1604
  Dihedral  :  4.453  30.927   1277
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.29 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.52 (0.25), residues: 1118
  helix:  1.42 (0.33), residues: 259
  sheet:  0.44 (0.27), residues: 354
  loop : -0.20 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.021   0.001   PHE B 532 
 TYR   0.020   0.001   TYR H  80 
 ARG   0.002   0.000   ARG R 457 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7031 (mm)
REVERT: L   69 THR cc_start: 0.7998 (t) cc_final: 0.7741 (p)
REVERT: R  357 ARG cc_start: 0.6798 (ttp-170) cc_final: 0.6485 (ttp-170)
REVERT: R  481 ASN cc_start: 0.7039 (t0) cc_final: 0.6829 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 143
  average time/residue: 0.1864
  time to fit residues: 38.6239
Evaluate side-chains
  141 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0980
   chunk 4 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 125 ASN
** B 356 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 = 0.4073 r_free = 0.4073 target = 0.173033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.140738 restraints weight = 11251.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.133398 restraints weight = 13825.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 77)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.130853 restraints weight = 12132.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   9226  Z= 0.297
  Angle     :  0.609  13.658  12527  Z= 0.313
  Chirality :  0.043   0.142   1367
  Planarity :  0.004   0.051   1604
  Dihedral  :  4.665  31.587   1277
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.77 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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 (0.25), residues: 1118
  helix:  1.39 (0.33), residues: 258
  sheet:  0.37 (0.27), residues: 355
  loop : -0.32 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP N  47 
 HIS   0.003   0.001   HIS L  95 
 PHE   0.022   0.002   PHE B 532 
 TYR   0.024   0.002   TYR H  80 
 ARG   0.003   0.000   ARG R 457 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7051 (mm)
REVERT: L   69 THR cc_start: 0.8032 (t) cc_final: 0.7768 (p)
  outliers start: 30
  outliers final: 26
  residues processed: 143
  average time/residue: 0.1810
  time to fit residues: 38.0988
Evaluate side-chains
  146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain R residue  401 VAL
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 54 optimal weight:    0.2980
   chunk 89 optimal weight:    0.0980
   chunk 101 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 90 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
** B 356 GLN ** 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 = 0.4126 r_free = 0.4126 target = 0.178623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.146503 restraints weight = 11284.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.143076 restraints weight = 12964.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.139643 restraints weight = 12004.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9226  Z= 0.166
  Angle     :  0.578  13.112  12527  Z= 0.296
  Chirality :  0.042   0.151   1367
  Planarity :  0.005   0.095   1604
  Dihedral  :  4.455  31.799   1277
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.70 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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 (0.25), residues: 1118
  helix:  1.46 (0.33), residues: 259
  sheet:  0.37 (0.27), residues: 354
  loop : -0.21 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.026   0.001   PHE B 259 
 TYR   0.020   0.001   TYR B 100 
 ARG   0.002   0.000   ARG N  45 

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

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

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2236 Ramachandran restraints generated.
    1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6849 (mm)
REVERT: L   69 THR cc_start: 0.8013 (t) cc_final: 0.7757 (p)
REVERT: R  357 ARG cc_start: 0.6838 (ttp-170) cc_final: 0.6524 (ttp-170)
  outliers start: 21
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1978
  time to fit residues: 41.2516
Evaluate side-chains
  142 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 MET
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   56 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   21 MET
Chi-restraints excluded: chain L residue   94 CYS
Chi-restraints excluded: chain L residue   95 HIS
Chi-restraints excluded: chain R residue  432 CYS
Chi-restraints excluded: chain R residue  461 LEU
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0980
   chunk 85 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   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 101 ASN
** B 356 GLN ** 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 = 0.4121 r_free = 0.4121 target = 0.177798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.144828 restraints weight = 11167.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139182 restraints weight = 13931.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 107)---------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.136248 restraints weight = 13143.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   9226  Z= 0.187
  Angle     :  0.585  13.301  12527  Z= 0.298
  Chirality :  0.042   0.162   1367
  Planarity :  0.005   0.095   1604
  Dihedral  :  4.420  31.665   1277
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.81 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.72 %
    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:  0.53 (0.25), residues: 1118
  helix:  1.52 (0.33), residues: 259
  sheet:  0.39 (0.27), residues: 350
  loop : -0.20 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP N  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.026   0.001   PHE B 259 
 TYR   0.019   0.001   TYR B 100 
 ARG   0.007   0.000   ARG N  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3103.20 seconds
wall clock time: 55 minutes 35.52 seconds (3335.52 seconds total)