Starting phenix.real_space_refine
on Thu Feb 13 14:14:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rxd_24729/02_2025/7rxd_24729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rxd_24729/02_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_24729/02_2025/7rxd_24729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rxd_24729/02_2025/7rxd_24729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rxd_24729/02_2025/7rxd_24729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rxd_24729/02_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-5592/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: 5.33, per 1000 atoms: 0.59
  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.43
  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: 3.35

  Time building geometry restraints manager: 2.71 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:             0.500
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.920
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.920
-------------------------------------------------------------------------------
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  : 1.055 
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: 0.2063
  time to fit residues: 41.6386
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  : 0.984 
-------------------------------------------------------------------------------
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 = 11861.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.176306 restraints weight = 17643.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177429 restraints weight = 12029.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.0993

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  : 1.016 
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: 0.2043
  time to fit residues: 41.1249
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  : 1.107 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 77 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.9588

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.193920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.164510 restraints weight = 11632.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.164496 restraints weight = 17455.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.166868 restraints weight = 15779.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.1206

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= 0.201
  Angle     :  0.530  13.410  12527  Z= 0.277
  Chirality :  0.041   0.134   1367
  Planarity :  0.004   0.089   1604
  Dihedral  :  4.282  31.458   1277
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.66 %
    Favored  : 88.30 %
  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:  0.82 (0.25), residues: 1118
  helix:  1.24 (0.32), residues: 265
  sheet:  0.67 (0.27), residues: 358
  loop :  0.21 (0.29), residues: 495

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   0.029   0.002   PHE B 510 
 TYR   0.024   0.001   TYR R 505 
 ARG   0.004   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
  143 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
REVERT: B  132 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7642 (tm-30)
REVERT: B  405 HIS cc_start: 0.8608 (t-90) cc_final: 0.8131 (t-170)
REVERT: B  532 PHE cc_start: 0.7438 (m-80) cc_final: 0.7188 (m-80)
REVERT: H    6 GLU cc_start: 0.6997 (mp0) cc_final: 0.6773 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 136
  average time/residue: 0.1976
  time to fit residues: 38.2162
Evaluate side-chains
  128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
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 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:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4290 r_free = 0.4290 target = 0.192549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.163158 restraints weight = 11706.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.159960 restraints weight = 13142.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.157316 restraints weight = 13509.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   9226  Z= 0.308
  Angle     :  0.580  11.969  12527  Z= 0.302
  Chirality :  0.043   0.197   1367
  Planarity :  0.005   0.080   1604
  Dihedral  :  4.505  30.141   1277
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.25 %
    Favored  : 84.89 %
  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:  0.77 (0.25), residues: 1118
  helix:  1.52 (0.33), residues: 252
  sheet:  0.68 (0.27), residues: 356
  loop : -0.02 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP N  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.016   0.002   PHE B 532 
 TYR   0.021   0.002   TYR R 505 
 ARG   0.003   0.000   ARG N  38 

*********************** 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
  147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 HIS cc_start: 0.8701 (t-90) cc_final: 0.8284 (t-170)
REVERT: B  532 PHE cc_start: 0.7616 (m-80) cc_final: 0.6852 (m-80)
REVERT: R  357 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.6489 (ttp-170)
  outliers start: 18
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1917
  time to fit residues: 38.4906
Evaluate side-chains
  131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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   89 GLU
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  478 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   chunk 98 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0270
   chunk 111 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.7640

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.203757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.163479 restraints weight = 11926.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.157802 restraints weight = 11260.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.156835 restraints weight = 9944.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9226  Z= 0.181
  Angle     :  0.540  14.810  12527  Z= 0.279
  Chirality :  0.041   0.170   1367
  Planarity :  0.004   0.061   1604
  Dihedral  :  4.334  30.828   1277
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 14.49 %
    Favored  : 83.85 %
  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:  0.84 (0.25), residues: 1118
  helix:  1.65 (0.33), residues: 252
  sheet:  0.62 (0.27), residues: 359
  loop :  0.05 (0.29), residues: 507

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   0.024   0.001   PHE B 532 
 TYR   0.016   0.001   TYR R 505 
 ARG   0.002   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: 16
    poor density    : 130
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: B  291 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6681 (mm)
REVERT: B  405 HIS cc_start: 0.8682 (t-90) cc_final: 0.8275 (t-170)
REVERT: B  485 LEU cc_start: 0.9161 (tp) cc_final: 0.8934 (tp)
REVERT: H  219 LYS cc_start: 0.7489 (tppt) cc_final: 0.7104 (tppt)
REVERT: R  357 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6664 (ttp-170)
  outliers start: 16
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1960
  time to fit residues: 38.9190
Evaluate side-chains
  134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
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   56 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  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:    0.9990
   chunk 109 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0970
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 110 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 283 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.203524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.163153 restraints weight = 11900.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.158329 restraints weight = 11455.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.157409 restraints weight = 8794.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9226  Z= 0.186
  Angle     :  0.532  14.145  12527  Z= 0.275
  Chirality :  0.041   0.147   1367
  Planarity :  0.004   0.055   1604
  Dihedral  :  4.244  30.141   1277
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.53 %
    Favored  : 82.71 %
  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:  0.85 (0.25), residues: 1118
  helix:  1.53 (0.33), residues: 260
  sheet:  0.61 (0.27), residues: 361
  loop :  0.12 (0.29), residues: 497

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   0.017   0.001   PHE B 510 
 TYR   0.020   0.001   TYR B 100 
 ARG   0.002   0.000   ARG N  38 

*********************** 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
  149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: L   69 THR cc_start: 0.8185 (t) cc_final: 0.7923 (p)
REVERT: R  351 TYR cc_start: 0.8055 (p90) cc_final: 0.7762 (p90)
  outliers start: 17
  outliers final: 13
  residues processed: 140
  average time/residue: 0.1956
  time to fit residues: 39.7361
Evaluate side-chains
  132 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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    5 VAL
Chi-restraints excluded: chain H residue   48 VAL
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   66 ASP
Chi-restraints excluded: chain L residue   95 HIS
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:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 93 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 324 ASN
** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 366 GLN
** L  95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 171 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.171937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.145465 restraints weight = 11458.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.138148 restraints weight = 13070.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 130)---------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.135562 restraints weight = 12600.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.089   9226  Z= 0.441
  Angle     :  0.675  16.474  12527  Z= 0.351
  Chirality :  0.046   0.197   1367
  Planarity :  0.005   0.049   1604
  Dihedral  :  4.894  32.340   1277
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.05 %
    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:  0.43 (0.25), residues: 1118
  helix:  1.17 (0.32), residues: 261
  sheet:  0.45 (0.27), residues: 355
  loop : -0.21 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP N  47 
 HIS   0.003   0.001   HIS N 125 
 PHE   0.032   0.002   PHE B 510 
 TYR   0.027   0.002   TYR L  97 
 ARG   0.004   0.001   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
  157 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.973 
Fit side-chains
REVERT: B  532 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7369 (m-80)
REVERT: L   69 THR cc_start: 0.8174 (t) cc_final: 0.7948 (p)
REVERT: L  147 ARG cc_start: 0.7296 (ttm110) cc_final: 0.7013 (mtp180)
REVERT: R  351 TYR cc_start: 0.8237 (p90) cc_final: 0.7966 (p90)
REVERT: R  357 ARG cc_start: 0.6708 (ttp-170) cc_final: 0.6456 (ttp-170)
  outliers start: 28
  outliers final: 20
  residues processed: 143
  average time/residue: 0.1988
  time to fit residues: 40.2184
Evaluate side-chains
  139 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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  532 PHE
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  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  151 LEU
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   12 VAL
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  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0050
   chunk 101 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.178541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.145914 restraints weight = 11388.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142715 restraints weight = 14090.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139540 restraints weight = 13344.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9226  Z= 0.173
  Angle     :  0.581  15.349  12527  Z= 0.299
  Chirality :  0.042   0.204   1367
  Planarity :  0.004   0.051   1604
  Dihedral  :  4.474  30.929   1277
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.18 %
    Favored  : 80.64 %
  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:  0.62 (0.25), residues: 1118
  helix:  1.39 (0.33), residues: 261
  sheet:  0.48 (0.27), residues: 348
  loop : -0.04 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP N  47 
 HIS   0.003   0.001   HIS L  95 
 PHE   0.019   0.001   PHE B 510 
 TYR   0.018   0.001   TYR B 100 
 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
  145 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.974 
Fit side-chains
REVERT: R  351 TYR cc_start: 0.8077 (p90) cc_final: 0.7811 (p90)
  outliers start: 21
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1884
  time to fit residues: 36.2106
Evaluate side-chains
  128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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  120 THR
Chi-restraints excluded: chain H residue  151 LEU
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  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:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0970
   chunk 110 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    1.1580

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.176058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.143986 restraints weight = 11175.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 140)---------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137474 restraints weight = 13680.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 143)---------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132191 restraints weight = 12690.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9226  Z= 0.222
  Angle     :  0.604  17.941  12527  Z= 0.308
  Chirality :  0.043   0.241   1367
  Planarity :  0.004   0.044   1604
  Dihedral  :  4.468  30.744   1277
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.98 %
    Favored  : 80.75 %
  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:  0.56 (0.25), residues: 1118
  helix:  1.39 (0.33), residues: 259
  sheet:  0.44 (0.26), residues: 354
  loop : -0.11 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.019   0.001   PHE B 510 
 TYR   0.020   0.001   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
  143 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.083 
Fit side-chains
REVERT: R  351 TYR cc_start: 0.8139 (p90) cc_final: 0.7848 (p90)
  outliers start: 22
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1862
  time to fit residues: 35.7814
Evaluate side-chains
  133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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    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  120 THR
Chi-restraints excluded: chain H residue  151 LEU
Chi-restraints excluded: chain H residue  175 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 N residue   48 VAL
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:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 101 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.178052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145359 restraints weight = 11241.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142759 restraints weight = 14012.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.138836 restraints weight = 11866.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
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      :  0.003   0.053   9226  Z= 0.176
  Angle     :  0.588  17.120  12527  Z= 0.299
  Chirality :  0.042   0.226   1367
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.346  30.321   1277
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.60 %
    Favored  : 80.43 %
  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:  0.59 (0.25), residues: 1118
  helix:  1.46 (0.33), residues: 259
  sheet:  0.40 (0.27), residues: 356
  loop : -0.07 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP N  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.016   0.001   PHE B 510 
 TYR   0.023   0.001   TYR H  80 
 ARG   0.002   0.000   ARG R 457 

********************** 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
  146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.862 
Fit side-chains
REVERT: R  351 TYR cc_start: 0.7970 (p90) cc_final: 0.7687 (p90)
REVERT: R  357 ARG cc_start: 0.6773 (ttp-170) cc_final: 0.6464 (ttp-170)
  outliers start: 19
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1957
  time to fit residues: 38.4004
Evaluate side-chains
  134 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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    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  120 THR
Chi-restraints excluded: chain H residue  151 LEU
Chi-restraints excluded: chain H residue  175 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  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:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 125 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 = 0.178288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.146765 restraints weight = 11179.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.144320 restraints weight = 13226.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.142051 restraints weight = 10641.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9226  Z= 0.185
  Angle     :  0.588  16.790  12527  Z= 0.300
  Chirality :  0.042   0.217   1367
  Planarity :  0.004   0.051   1604
  Dihedral  :  4.333  29.910   1277
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.60 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    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:  0.61 (0.25), residues: 1118
  helix:  1.51 (0.33), residues: 259
  sheet:  0.43 (0.27), residues: 356
  loop : -0.09 (0.29), residues: 503

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   0.023   0.001   PHE R 374 
 TYR   0.018   0.001   TYR B 100 
 ARG   0.003   0.000   ARG R 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3017.33 seconds
wall clock time: 54 minutes 43.16 seconds (3283.16 seconds total)