Starting phenix.real_space_refine
on Tue Mar  3 17:21:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pcq_13325/03_2026/7pcq_13325_neut.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      22      5.16       5
     C    4734      2.51       5
     N    1246      2.21       5
     O    1344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7350
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
    Chain: "B"
      Number of atoms: 1134
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
      Conformer: "B"
        Number of residues, atoms: 146, 1123
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
          bond proxies already assigned to first conformer: 1141
    Chain: "C"
      Number of atoms: 1078
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
      Conformer: "B"
        Number of residues, atoms: 141, 1069
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 133}
          bond proxies already assigned to first conformer: 1087
    Chain: "D"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1111
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 138}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 2786
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 337, 2777
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324}
      Conformer: "B"
        Number of residues, atoms: 337, 2777
          Classifications: {'peptide': 337}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 324}
          bond proxies already assigned to first conformer: 2823
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG B 104 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 104 " occ=0.50
    residue:
      pdb=" N  ALYS C  56 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  56 " occ=0.50
    residue:
      pdb=" N  ALYS E 232 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS E 232 " occ=0.50
  Time building chain proxies: 2.75, per 1000 atoms: 0.37
  Number of scatterers: 7350
  At special positions: 0
  Unit cell: (74.98, 99.104, 97.148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      22     16.00
     O    1344      8.00
     N    1246      7.00
     C    4734      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 447.6 milliseconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      64.0% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 3.619A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 138
    Processing helix  chain 'B' and resid 4 through 18
      removed outlier: 3.806A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 35
      removed outlier: 3.637A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLY B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  28 " --> pdb=" O   GLY B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 41
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 77
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 3.773A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N  AARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 3 through 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 90
      removed outlier: 5.372A  pdb=" N   ALA C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 5.709A  pdb=" N   LEU C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 113
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.730A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 3.889A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 57
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 81 through 95
      removed outlier: 5.140A  pdb=" N   THR D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   LEU D  88 " --> pdb=" O   THR D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 119
      removed outlier: 3.781A  pdb=" N   PHE D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 142
    Processing helix  chain 'E' and resid 128 through 135
      removed outlier: 4.049A  pdb=" N   LYS E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASN E 135 " --> pdb=" O   GLU E 131 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 163 through 169
    Processing helix  chain 'E' and resid 263 through 267
    Processing helix  chain 'E' and resid 269 through 285
      Proline residue:  E 281  - end of helix
    Processing helix  chain 'E' and resid 287 through 302
      removed outlier: 3.516A  pdb=" N   LYS E 297 " --> pdb=" O   TYR E 293 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ASP E 300 " --> pdb=" O   ASN E 296 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS E 301 " --> pdb=" O   LYS E 297 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 303 through 332
      removed outlier: 4.407A  pdb=" N   ALA E 308 " --> pdb=" O   GLU E 304 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   GLU E 309 " --> pdb=" O   LYS E 305 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 361 through 365
    Processing helix  chain 'E' and resid 451 through 460
      removed outlier: 3.747A  pdb=" N   LYS E 456 " --> pdb=" O   GLU E 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 148 through 151
      removed outlier: 5.814A  pdb=" N   GLY E 188 " --> pdb=" O   PRO E 173 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ARG E 224 " --> pdb=" O   LEU E 211 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   LEU E 211 " --> pdb=" O   ARG E 224 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   SER E 226 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ILE E 209 " --> pdb=" O   SER E 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 153 through 156
      removed outlier: 6.057A  pdb=" N   HIS E 241 " --> pdb=" O   TRP E 195 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   TRP E 195 " --> pdb=" O   HIS E 241 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   VAL E 200 " --> pdb=" O   LEU E 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 153 through 156
    Processing sheet with id=AA4, first strand: chain 'E' and resid 346 through 348
      removed outlier: 4.126A  pdb=" N   ILE E 371 " --> pdb=" O   THR E 348 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS E 368 " --> pdb=" O   THR E 387 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   THR E 387 " --> pdb=" O   LYS E 368 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLU E 385 " --> pdb=" O   PRO E 370 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER E 406 " --> pdb=" O   THR E 415 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE E 417 " --> pdb=" O   THR E 404 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   THR E 404 " --> pdb=" O   ILE E 417 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 350 through 353
      removed outlier: 7.274A  pdb=" N   ASP E 428 " --> pdb=" O   VAL E 397 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL E 397 " --> pdb=" O   ASP E 428 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ILE E 430 " --> pdb=" O   PHE E 395 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   PHE E 395 " --> pdb=" O   ILE E 430 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   LYS E 432 " --> pdb=" O   LYS E 393 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1340 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 2475
        1.37 -     1.55: 5010
        1.55 -     1.72: 14
        1.72 -     1.90: 38
        1.90 -     2.08: 16
  Bond restraints: 7553
  Sorted by residual:
  bond pdb=" CA  SER E 169 "
       pdb=" CB  SER E 169 "
    ideal  model  delta    sigma   weight residual
    1.527  1.465  0.062 1.36e-02 5.41e+03 2.07e+01
  bond pdb=" C   VAL D 109 "
       pdb=" O   VAL D 109 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.19e-02 7.06e+03 1.74e+01
  bond pdb=" N   VAL E 356 "
       pdb=" CA  VAL E 356 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 9.10e-03 1.21e+04 1.62e+01
  bond pdb=" N   VAL E 234 "
       pdb=" CA  VAL E 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.041 1.11e-02 8.12e+03 1.34e+01
  bond pdb=" C3D HEM A 201 "
       pdb=" CAD HEM A 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.472  0.072 2.00e-02 2.50e+03 1.30e+01
  ... (remaining 7548 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8730
        2.27 -     4.53: 1486
        4.53 -     6.80: 61
        6.80 -     9.06: 5
        9.06 -    11.33: 11
  Bond angle restraints: 10293
  Sorted by residual:
  angle pdb=" CA  GLN D 127 "
        pdb=" C   GLN D 127 "
        pdb=" O   GLN D 127 "
      ideal   model   delta    sigma   weight residual
     120.55  115.25    5.30 1.06e+00 8.90e-01 2.50e+01
  angle pdb=" CA  GLN B 127 "
        pdb=" C   GLN B 127 "
        pdb=" O   GLN B 127 "
      ideal   model   delta    sigma   weight residual
     120.55  115.29    5.26 1.06e+00 8.90e-01 2.46e+01
  angle pdb=" N   ASP E 364 "
        pdb=" CA  ASP E 364 "
        pdb=" C   ASP E 364 "
      ideal   model   delta    sigma   weight residual
     111.28  105.97    5.31 1.09e+00 8.42e-01 2.37e+01
  angle pdb=" CA  PHE C  43 "
        pdb=" C   PHE C  43 "
        pdb=" N   PRO C  44 "
      ideal   model   delta    sigma   weight residual
     117.78  122.72   -4.94 1.06e+00 8.90e-01 2.17e+01
  angle pdb=" CA  PHE A  43 "
        pdb=" C   PHE A  43 "
        pdb=" N   PRO A  44 "
      ideal   model   delta    sigma   weight residual
     117.78  122.69   -4.91 1.06e+00 8.90e-01 2.14e+01
  ... (remaining 10288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4092
       17.93 -    35.85: 263
       35.85 -    53.78: 57
       53.78 -    71.71: 10
       71.71 -    89.63: 13
  Dihedral angle restraints: 4435
    sinusoidal: 1762
      harmonic: 2673
  Sorted by residual:
  dihedral pdb=" C2C HEM A 201 "
           pdb=" C3C HEM A 201 "
           pdb=" CAC HEM A 201 "
           pdb=" CBC HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -85.15   85.15     2      1.00e+01 1.00e-02 4.77e+01
  dihedral pdb=" C2C HEM C 201 "
           pdb=" C3C HEM C 201 "
           pdb=" CAC HEM C 201 "
           pdb=" CBC HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -72.45   72.45     2      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" C2B HEM C 201 "
           pdb=" C3B HEM C 201 "
           pdb=" CAB HEM C 201 "
           pdb=" CBB HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  109.92   70.08     2      1.00e+01 1.00e-02 4.24e+01
  ... (remaining 4432 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 505
       0.062 -    0.123: 342
       0.123 -    0.185: 219
       0.185 -    0.246: 40
       0.246 -    0.307: 8
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  VAL E 176 "
            pdb=" N   VAL E 176 "
            pdb=" C   VAL E 176 "
            pdb=" CB  VAL E 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.75   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  ARG E 130 "
            pdb=" N   ARG E 130 "
            pdb=" C   ARG E 130 "
            pdb=" CB  ARG E 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" CB  VAL A  70 "
            pdb=" CA  VAL A  70 "
            pdb=" CG1 VAL A  70 "
            pdb=" CG2 VAL A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1111 not shown)

  Planarity restraints: 1298
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR E 231 "    0.027 2.00e-02 2.50e+03   5.45e-02 2.98e+01
        pdb=" C   THR E 231 "   -0.094 2.00e-02 2.50e+03
        pdb=" O   THR E 231 "    0.035 2.00e-02 2.50e+03
        pdb=" N  BLYS E 232 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA AARG B 104 "   -0.026 2.00e-02 2.50e+03   5.42e-02 2.93e+01
        pdb=" C  AARG B 104 "    0.094 2.00e-02 2.50e+03
        pdb=" O  AARG B 104 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   LEU B 105 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 266 "    0.026 2.00e-02 2.50e+03   5.33e-02 2.84e+01
        pdb=" C   LYS E 266 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   LYS E 266 "    0.034 2.00e-02 2.50e+03
        pdb=" N   PHE E 267 "    0.032 2.00e-02 2.50e+03
  ... (remaining 1295 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 4121
        3.03 -     3.49: 7699
        3.49 -     3.96: 12608
        3.96 -     4.43: 14872
        4.43 -     4.90: 22478
  Nonbonded interactions: 61778
  Sorted by model distance:
  nonbonded pdb=" N   THR A 118 "
            pdb=" O   THR A 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" N   THR C 118 "
            pdb=" O   THR C 118 "
     model   vdw
     2.557 2.496
  nonbonded pdb=" O   TYR C 140 "
            pdb=" C   ARG C 141 "
     model   vdw
     2.557 3.270
  nonbonded pdb=" O   TYR D  35 "
            pdb=" OG1 THR D  38 "
     model   vdw
     2.564 3.040
  nonbonded pdb=" O   TYR E 391 "
            pdb=" N   HIS E 434 "
     model   vdw
     2.567 3.120
  ... (remaining 61773 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 55 or resid 57 through 201))
  selection = (chain 'C' and (resid 1 through 55 or resid 57 through 201))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 64 or (resid 65 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 66 through 103 or resid 105 through 119 or (re \ 
sid 120 through 121 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 122 through 201))
  selection = (chain 'D' and (resid 1 through 103 or resid 105 through 201))
}

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=0.00 max=1.00 mean=0.99
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:             3.630
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.730
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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      :  0.014   0.246   7557  Z= 0.937
  Angle     :  1.548  11.328  10293  Z= 1.156
  Chirality :  0.098   0.307   1114
  Planarity :  0.008   0.055   1298
  Dihedral  : 13.616  89.634   2707
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  5.58 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.27), residues: 910
  helix:  2.24 (0.22), residues: 525
  sheet: -0.47 (0.57), residues: 78
  loop : -0.33 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 414 
 TYR   0.015   0.002   TYR E 251 
 PHE   0.010   0.002   PHE E 225 
 TRP   0.013   0.002   TRP C  14 
 HIS   0.005   0.001   HIS C 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.01284 ( 7553)
  covalent geometry    : angle       1.54795 (10293)
  hydrogen bonds       : bond        0.18934 (  471)
  hydrogen bonds       : angle       7.38637 ( 1340)
  Misc. bond           : bond        0.20433 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8609 (tt0) cc_final: 0.8050 (tt0)
REVERT: B    7 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8493 (mt-10)
REVERT: B   35 TYR cc_start: 0.8799 (m-80) cc_final: 0.8596 (m-10)
REVERT: B   47 ASP cc_start: 0.8397 (t0) cc_final: 0.8155 (t0)
REVERT: B   98 VAL cc_start: 0.9513 (t) cc_final: 0.9114 (p)
REVERT: B  105 LEU cc_start: 0.9260 (mt) cc_final: 0.9059 (mt)
REVERT: B  108 ASN cc_start: 0.9230 (m-40) cc_final: 0.8906 (t0)
REVERT: B  127 GLN cc_start: 0.8895 (tt0) cc_final: 0.8232 (tm-30)
REVERT: B  131 GLN cc_start: 0.8995 (mm110) cc_final: 0.8486 (mm110)
REVERT: C   14 TRP cc_start: 0.8183 (t-100) cc_final: 0.7828 (t-100)
REVERT: D   31 LEU cc_start: 0.9406 (tp) cc_final: 0.9198 (tt)
REVERT: D   38 THR cc_start: 0.8975 (p) cc_final: 0.8725 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 175
  average time/residue: 0.1027
  time to fit residues: 23.3857
Evaluate side-chains
  97 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
B  63 HIS
C  58 HIS
D  39 GLN
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 339 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.033098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2390 r_free = 0.2390 target = 0.022337 restraints weight = 196835.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2442 r_free = 0.2442 target = 0.023924 restraints weight = 60800.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.025149 restraints weight = 33423.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.025955 restraints weight = 22263.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.026637 restraints weight = 16945.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.2531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2528 r_free = 0.2528    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2526 r_free = 0.2526    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.2526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   7557  Z= 0.145
  Angle     :  0.631   6.603  10293  Z= 0.325
  Chirality :  0.042   0.155   1114
  Planarity :  0.005   0.039   1298
  Dihedral  :  8.724  89.045   1005
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.38 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.27), residues: 910
  helix:  2.71 (0.22), residues: 522
  sheet:  0.19 (0.56), residues: 85
  loop :  0.28 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 403 
 TYR   0.011   0.001   TYR B 130 
 PHE   0.016   0.002   PHE E 178 
 TRP   0.024   0.002   TRP C  14 
 HIS   0.005   0.001   HIS E 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7553)
  covalent geometry    : angle       0.63080 (10293)
  hydrogen bonds       : bond        0.03637 (  471)
  hydrogen bonds       : angle       5.16035 ( 1340)
  Misc. bond           : bond        0.05937 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9137 (t0) cc_final: 0.8931 (t0)
REVERT: B    7 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9215 (mt-10)
REVERT: B   21 ASP cc_start: 0.9424 (p0) cc_final: 0.8312 (p0)
REVERT: B   47 ASP cc_start: 0.8974 (t0) cc_final: 0.8622 (t0)
REVERT: B  108 ASN cc_start: 0.9392 (m-40) cc_final: 0.9078 (t0)
REVERT: B  127 GLN cc_start: 0.9473 (tt0) cc_final: 0.8677 (tm-30)
REVERT: B  131 GLN cc_start: 0.9434 (mm110) cc_final: 0.9066 (mm110)
REVERT: D    6 GLU cc_start: 0.9241 (pm20) cc_final: 0.9037 (pm20)
REVERT: D   26 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8949 (mm-30)
REVERT: D  127 GLN cc_start: 0.9779 (tt0) cc_final: 0.9197 (tm-30)
REVERT: D  144 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8887 (mmtp)
REVERT: E  155 MET cc_start: 0.8903 (mmm) cc_final: 0.8572 (mmp)
REVERT: E  190 GLN cc_start: 0.9364 (mt0) cc_final: 0.8752 (mp10)
REVERT: E  439 ASP cc_start: 0.9204 (t0) cc_final: 0.8991 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 109
  average time/residue: 0.0917
  time to fit residues: 13.5462
Evaluate side-chains
  90 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0370
   chunk 61 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 76 optimal weight:    0.3980
   chunk 58 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
B  63 HIS
B 102 ASN
C 122 HIS
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 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 = 0.2791 r_free = 0.2791 target = 0.032708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2403 r_free = 0.2403 target = 0.022793 restraints weight = 192778.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2457 r_free = 0.2457 target = 0.024334 restraints weight = 58832.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2501 r_free = 0.2501 target = 0.025538 restraints weight = 32208.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2530 r_free = 0.2530 target = 0.026337 restraints weight = 21451.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.027025 restraints weight = 16149.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2534 r_free = 0.2534    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2530 r_free = 0.2530    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2530
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105   7557  Z= 0.115
  Angle     :  0.596   9.235  10293  Z= 0.299
  Chirality :  0.040   0.145   1114
  Planarity :  0.004   0.039   1298
  Dihedral  :  8.430  89.982   1004
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.16 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.28), residues: 910
  helix:  2.67 (0.22), residues: 523
  sheet:  0.15 (0.53), residues: 101
  loop :  0.37 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 403 
 TYR   0.012   0.001   TYR B  35 
 PHE   0.009   0.001   PHE E 178 
 TRP   0.014   0.002   TRP A  14 
 HIS   0.004   0.001   HIS E 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7553)
  covalent geometry    : angle       0.59556 (10293)
  hydrogen bonds       : bond        0.03175 (  471)
  hydrogen bonds       : angle       4.82012 ( 1340)
  Misc. bond           : bond        0.07019 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9151 (ttm)
REVERT: A   94 ASP cc_start: 0.9230 (t0) cc_final: 0.8786 (t0)
REVERT: B    7 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9151 (mt-10)
REVERT: B   21 ASP cc_start: 0.8967 (p0) cc_final: 0.8099 (p0)
REVERT: B   22 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8776 (mp0)
REVERT: B   47 ASP cc_start: 0.9087 (t0) cc_final: 0.8786 (t0)
REVERT: B  108 ASN cc_start: 0.9410 (m-40) cc_final: 0.9137 (t0)
REVERT: B  127 GLN cc_start: 0.9496 (tt0) cc_final: 0.8696 (tm-30)
REVERT: B  131 GLN cc_start: 0.9379 (mm110) cc_final: 0.9024 (mm110)
REVERT: D   22 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: D   26 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8947 (mm-30)
REVERT: D   55 MET cc_start: 0.9047 (mmp) cc_final: 0.8746 (mmp)
REVERT: D   71 PHE cc_start: 0.9688 (m-80) cc_final: 0.9309 (m-80)
REVERT: D   99 ASP cc_start: 0.8742 (t0) cc_final: 0.8142 (t0)
REVERT: D  104 ARG cc_start: 0.9528 (ptm-80) cc_final: 0.9316 (ptp-170)
REVERT: D  127 GLN cc_start: 0.9757 (tt0) cc_final: 0.9196 (tm-30)
REVERT: E  155 MET cc_start: 0.8753 (mmm) cc_final: 0.7745 (mmp)
REVERT: E  254 MET cc_start: 0.9444 (ttt) cc_final: 0.9095 (tpt)
REVERT: E  354 GLU cc_start: 0.9327 (tm-30) cc_final: 0.8985 (mp0)
REVERT: E  384 MET cc_start: 0.9647 (ttm) cc_final: 0.9384 (ttm)
REVERT: E  439 ASP cc_start: 0.9252 (t0) cc_final: 0.8984 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0860
  time to fit residues: 11.7887
Evaluate side-chains
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  382 MET
Chi-restraints excluded: chain E residue  386 THR
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  63 HIS
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 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 = 0.2766 r_free = 0.2766 target = 0.031884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2375 r_free = 0.2375 target = 0.022209 restraints weight = 181099.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2431 r_free = 0.2431 target = 0.023720 restraints weight = 57223.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2471 r_free = 0.2471 target = 0.024780 restraints weight = 31457.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.025616 restraints weight = 21586.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.026144 restraints weight = 15997.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.2498
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2498 r_free = 0.2498    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2497 r_free = 0.2497    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.4211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   7557  Z= 0.114
  Angle     :  0.579   9.908  10293  Z= 0.287
  Chirality :  0.039   0.162   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.418  86.191   1004
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.90 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.28), residues: 910
  helix:  2.91 (0.22), residues: 509
  sheet:  0.25 (0.53), residues: 102
  loop :  0.53 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 403 
 TYR   0.017   0.001   TYR B  35 
 PHE   0.010   0.001   PHE E 178 
 TRP   0.014   0.002   TRP A  14 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7553)
  covalent geometry    : angle       0.57927 (10293)
  hydrogen bonds       : bond        0.02953 (  471)
  hydrogen bonds       : angle       4.59187 ( 1340)
  Misc. bond           : bond        0.08023 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.9254 (t0) cc_final: 0.8755 (t0)
REVERT: B    7 GLU cc_start: 0.9503 (mt-10) cc_final: 0.9081 (mt-10)
REVERT: B   21 ASP cc_start: 0.9002 (p0) cc_final: 0.8176 (p0)
REVERT: B   22 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8698 (mm-30)
REVERT: B   47 ASP cc_start: 0.9148 (t0) cc_final: 0.8868 (t0)
REVERT: B  108 ASN cc_start: 0.9394 (m-40) cc_final: 0.9111 (t0)
REVERT: B  127 GLN cc_start: 0.9481 (tt0) cc_final: 0.8713 (tm-30)
REVERT: B  131 GLN cc_start: 0.9360 (mm110) cc_final: 0.9022 (mm110)
REVERT: C   32 MET cc_start: 0.9593 (ttm) cc_final: 0.9293 (mmm)
REVERT: C   68 ASN cc_start: 0.9532 (t0) cc_final: 0.9306 (t0)
REVERT: D   22 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: D   26 GLU cc_start: 0.9446 (mm-30) cc_final: 0.8996 (mm-30)
REVERT: D   55 MET cc_start: 0.9175 (mmp) cc_final: 0.8891 (mmp)
REVERT: D   99 ASP cc_start: 0.8885 (t0) cc_final: 0.8415 (t0)
REVERT: D  127 GLN cc_start: 0.9750 (tt0) cc_final: 0.9195 (tm-30)
REVERT: E  155 MET cc_start: 0.8743 (mmm) cc_final: 0.7788 (mmp)
REVERT: E  254 MET cc_start: 0.9450 (ttt) cc_final: 0.9107 (tpt)
REVERT: E  342 MET cc_start: 0.9162 (tpp) cc_final: 0.8927 (tpp)
REVERT: E  392 TRP cc_start: 0.9163 (m100) cc_final: 0.8493 (m100)
REVERT: E  439 ASP cc_start: 0.9325 (t0) cc_final: 0.9083 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0893
  time to fit residues: 11.6766
Evaluate side-chains
  91 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain C residue  105 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 64 optimal weight:    0.4980
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.030515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2331 r_free = 0.2331 target = 0.020943 restraints weight = 215783.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.022396 restraints weight = 61815.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2426 r_free = 0.2426 target = 0.023479 restraints weight = 33118.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2460 r_free = 0.2460 target = 0.024277 restraints weight = 22285.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2478 r_free = 0.2478 target = 0.024756 restraints weight = 16475.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2465 r_free = 0.2465    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2464 r_free = 0.2464    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134   7557  Z= 0.132
  Angle     :  0.602   9.763  10293  Z= 0.294
  Chirality :  0.040   0.331   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.455  89.024   1004
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.38 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.28), residues: 910
  helix:  2.81 (0.22), residues: 523
  sheet:  0.50 (0.55), residues: 98
  loop :  0.33 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 403 
 TYR   0.017   0.001   TYR B  35 
 PHE   0.019   0.001   PHE E 418 
 TRP   0.014   0.002   TRP A  14 
 HIS   0.004   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7553)
  covalent geometry    : angle       0.60158 (10293)
  hydrogen bonds       : bond        0.02907 (  471)
  hydrogen bonds       : angle       4.49032 ( 1340)
  Misc. bond           : bond        0.09793 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9356 (tt0) cc_final: 0.8788 (tt0)
REVERT: A   94 ASP cc_start: 0.9375 (t0) cc_final: 0.8922 (t0)
REVERT: A  104 CYS cc_start: 0.9783 (OUTLIER) cc_final: 0.9525 (t)
REVERT: B    6 GLU cc_start: 0.9571 (pm20) cc_final: 0.9092 (pm20)
REVERT: B   21 ASP cc_start: 0.9074 (p0) cc_final: 0.8209 (p0)
REVERT: B   22 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8728 (mm-30)
REVERT: B   47 ASP cc_start: 0.9196 (t0) cc_final: 0.8983 (t0)
REVERT: B   73 ASP cc_start: 0.9389 (m-30) cc_final: 0.9057 (t0)
REVERT: B  127 GLN cc_start: 0.9513 (tt0) cc_final: 0.8779 (tm-30)
REVERT: B  131 GLN cc_start: 0.9380 (mm110) cc_final: 0.9154 (mm110)
REVERT: C   68 ASN cc_start: 0.9546 (t0) cc_final: 0.9313 (t0)
REVERT: D   22 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: D   26 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8985 (mm-30)
REVERT: D   55 MET cc_start: 0.9284 (mmp) cc_final: 0.9014 (mmp)
REVERT: D   71 PHE cc_start: 0.9663 (m-80) cc_final: 0.9381 (m-80)
REVERT: D   99 ASP cc_start: 0.8957 (t0) cc_final: 0.8567 (t0)
REVERT: D  127 GLN cc_start: 0.9744 (tt0) cc_final: 0.9197 (tm-30)
REVERT: E  439 ASP cc_start: 0.9436 (t0) cc_final: 0.9231 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0887
  time to fit residues: 10.8007
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 62 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.030493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2318 r_free = 0.2318 target = 0.020467 restraints weight = 193595.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2370 r_free = 0.2370 target = 0.021881 restraints weight = 59305.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2409 r_free = 0.2409 target = 0.022912 restraints weight = 32758.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2439 r_free = 0.2439 target = 0.023655 restraints weight = 22297.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.024169 restraints weight = 17011.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.2442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2442 r_free = 0.2442    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2442 r_free = 0.2442    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.137   7557  Z= 0.123
  Angle     :  0.618  10.970  10293  Z= 0.300
  Chirality :  0.040   0.305   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.398  88.290   1004
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.90 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.28), residues: 910
  helix:  2.78 (0.22), residues: 521
  sheet:  0.66 (0.56), residues: 98
  loop :  0.29 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 403 
 TYR   0.014   0.001   TYR C 140 
 PHE   0.016   0.001   PHE E 418 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7553)
  covalent geometry    : angle       0.61843 (10293)
  hydrogen bonds       : bond        0.02874 (  471)
  hydrogen bonds       : angle       4.46939 ( 1340)
  Misc. bond           : bond        0.09146 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9355 (tt0) cc_final: 0.8652 (tt0)
REVERT: A   30 GLU cc_start: 0.9527 (pt0) cc_final: 0.9067 (tt0)
REVERT: A   94 ASP cc_start: 0.9371 (t0) cc_final: 0.8913 (t0)
REVERT: A  104 CYS cc_start: 0.9745 (OUTLIER) cc_final: 0.9427 (t)
REVERT: B   21 ASP cc_start: 0.9087 (p0) cc_final: 0.8181 (p0)
REVERT: B   22 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8676 (mm-30)
REVERT: B   73 ASP cc_start: 0.9356 (m-30) cc_final: 0.9069 (t0)
REVERT: B  127 GLN cc_start: 0.9501 (tt0) cc_final: 0.8700 (tm-30)
REVERT: B  131 GLN cc_start: 0.9419 (mm110) cc_final: 0.9122 (mm-40)
REVERT: C   68 ASN cc_start: 0.9546 (t0) cc_final: 0.9318 (t0)
REVERT: D   22 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: D   26 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9027 (mm-30)
REVERT: D   55 MET cc_start: 0.9295 (mmp) cc_final: 0.9026 (mmp)
REVERT: D   71 PHE cc_start: 0.9669 (m-80) cc_final: 0.9392 (m-80)
REVERT: D   99 ASP cc_start: 0.8965 (t0) cc_final: 0.8465 (t0)
REVERT: D  127 GLN cc_start: 0.9752 (tt0) cc_final: 0.9205 (tm-30)
REVERT: D  132 LYS cc_start: 0.9681 (mtpp) cc_final: 0.9280 (mtmm)
REVERT: E  124 MET cc_start: 0.7616 (mmm) cc_final: 0.6808 (mmm)
REVERT: E  155 MET cc_start: 0.8809 (mmm) cc_final: 0.8557 (mmp)
REVERT: E  254 MET cc_start: 0.9528 (ttt) cc_final: 0.9318 (ttt)
REVERT: E  396 MET cc_start: 0.9208 (tpp) cc_final: 0.8922 (tpp)
  outliers start: 11
  outliers final: 8
  residues processed: 91
  average time/residue: 0.0896
  time to fit residues: 11.1522
Evaluate side-chains
  87 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 49 optimal weight:    0.3980
   chunk 58 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 15 optimal weight:    0.4980
   chunk 64 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.029846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2298 r_free = 0.2298 target = 0.019978 restraints weight = 192667.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2351 r_free = 0.2351 target = 0.021373 restraints weight = 59294.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2391 r_free = 0.2391 target = 0.022404 restraints weight = 32600.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2422 r_free = 0.2422 target = 0.023156 restraints weight = 22050.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2440 r_free = 0.2440 target = 0.023612 restraints weight = 16751.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.2422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2422
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2422 r_free = 0.2422    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2422 r_free = 0.2422    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8894
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.140   7557  Z= 0.129
  Angle     :  0.620  11.295  10293  Z= 0.302
  Chirality :  0.040   0.287   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.275  85.651   1004
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.68 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.28), residues: 910
  helix:  2.77 (0.22), residues: 523
  sheet:  0.61 (0.56), residues: 98
  loop :  0.30 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 403 
 TYR   0.015   0.001   TYR C 140 
 PHE   0.016   0.001   PHE E 418 
 TRP   0.011   0.001   TRP A  14 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7553)
  covalent geometry    : angle       0.62002 (10293)
  hydrogen bonds       : bond        0.02858 (  471)
  hydrogen bonds       : angle       4.44269 ( 1340)
  Misc. bond           : bond        0.09504 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.9362 (tt0) cc_final: 0.8659 (tt0)
REVERT: A   30 GLU cc_start: 0.9509 (pt0) cc_final: 0.9003 (tt0)
REVERT: A   68 ASN cc_start: 0.9757 (t0) cc_final: 0.9501 (t0)
REVERT: A   94 ASP cc_start: 0.9369 (t0) cc_final: 0.8918 (t0)
REVERT: A  104 CYS cc_start: 0.9738 (OUTLIER) cc_final: 0.9413 (t)
REVERT: B   21 ASP cc_start: 0.9064 (p0) cc_final: 0.8111 (p0)
REVERT: B   22 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: B   73 ASP cc_start: 0.9335 (m-30) cc_final: 0.9047 (t0)
REVERT: B  121 GLU cc_start: 0.9119 (tp30) cc_final: 0.8714 (tp30)
REVERT: B  127 GLN cc_start: 0.9505 (tt0) cc_final: 0.8769 (tm-30)
REVERT: C   68 ASN cc_start: 0.9564 (t0) cc_final: 0.9340 (t0)
REVERT: C  116 GLU cc_start: 0.8965 (pm20) cc_final: 0.8702 (pm20)
REVERT: D   22 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: D   26 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9041 (mm-30)
REVERT: D   55 MET cc_start: 0.9327 (mmp) cc_final: 0.9059 (mmp)
REVERT: D   71 PHE cc_start: 0.9647 (m-80) cc_final: 0.9323 (m-80)
REVERT: D   99 ASP cc_start: 0.9000 (t0) cc_final: 0.8525 (t0)
REVERT: D  127 GLN cc_start: 0.9751 (tt0) cc_final: 0.9217 (tm-30)
REVERT: D  132 LYS cc_start: 0.9688 (mtpp) cc_final: 0.9286 (mtmm)
REVERT: E  124 MET cc_start: 0.7745 (mmm) cc_final: 0.7077 (mmm)
REVERT: E  155 MET cc_start: 0.8797 (mmm) cc_final: 0.8517 (mmp)
REVERT: E  384 MET cc_start: 0.9730 (ttm) cc_final: 0.9480 (ttm)
  outliers start: 11
  outliers final: 9
  residues processed: 89
  average time/residue: 0.1019
  time to fit residues: 12.3302
Evaluate side-chains
  88 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:    0.0670
   chunk 81 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0010
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.6126

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.030537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2332 r_free = 0.2332 target = 0.020625 restraints weight = 184517.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2384 r_free = 0.2384 target = 0.022050 restraints weight = 58308.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2422 r_free = 0.2422 target = 0.023059 restraints weight = 32334.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2453 r_free = 0.2453 target = 0.023816 restraints weight = 22161.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2474 r_free = 0.2474 target = 0.024347 restraints weight = 16820.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2463 r_free = 0.2463    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2463 r_free = 0.2463    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.100   7557  Z= 0.109
  Angle     :  0.616  11.888  10293  Z= 0.299
  Chirality :  0.040   0.288   1114
  Planarity :  0.004   0.046   1298
  Dihedral  :  8.089  85.435   1004
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.94 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.28), residues: 910
  helix:  2.71 (0.22), residues: 525
  sheet:  0.61 (0.56), residues: 98
  loop :  0.28 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 403 
 TYR   0.016   0.001   TYR C 140 
 PHE   0.015   0.001   PHE E 418 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7553)
  covalent geometry    : angle       0.61624 (10293)
  hydrogen bonds       : bond        0.02691 (  471)
  hydrogen bonds       : angle       4.37812 ( 1340)
  Misc. bond           : bond        0.06476 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9766 (t0) cc_final: 0.9529 (t0)
REVERT: A   94 ASP cc_start: 0.9316 (t0) cc_final: 0.8850 (t0)
REVERT: A  104 CYS cc_start: 0.9679 (OUTLIER) cc_final: 0.9414 (t)
REVERT: B   21 ASP cc_start: 0.9075 (p0) cc_final: 0.8127 (p0)
REVERT: B   22 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: B   26 GLU cc_start: 0.9297 (tp30) cc_final: 0.9088 (tp30)
REVERT: B  121 GLU cc_start: 0.9132 (tp30) cc_final: 0.8701 (tp30)
REVERT: B  127 GLN cc_start: 0.9478 (tt0) cc_final: 0.8690 (tm-30)
REVERT: B  131 GLN cc_start: 0.9403 (mm110) cc_final: 0.9021 (mm110)
REVERT: C   68 ASN cc_start: 0.9561 (t0) cc_final: 0.9340 (t0)
REVERT: C  116 GLU cc_start: 0.8946 (pm20) cc_final: 0.8726 (pm20)
REVERT: D   22 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: D   26 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9041 (mm-30)
REVERT: D   55 MET cc_start: 0.9331 (mmp) cc_final: 0.9081 (mmp)
REVERT: D   71 PHE cc_start: 0.9645 (m-80) cc_final: 0.9301 (m-80)
REVERT: D   99 ASP cc_start: 0.8981 (t0) cc_final: 0.8494 (t0)
REVERT: D  127 GLN cc_start: 0.9755 (tt0) cc_final: 0.9118 (tm-30)
REVERT: D  132 LYS cc_start: 0.9686 (mtpp) cc_final: 0.9289 (mtmm)
REVERT: E  124 MET cc_start: 0.7753 (mmm) cc_final: 0.7128 (mmm)
REVERT: E  384 MET cc_start: 0.9737 (ttm) cc_final: 0.9506 (ttm)
REVERT: E  392 TRP cc_start: 0.9211 (m100) cc_final: 0.8537 (m100)
  outliers start: 10
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0924
  time to fit residues: 11.3798
Evaluate side-chains
  85 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 CYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue  112 CYS
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0060
   chunk 84 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.030740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2338 r_free = 0.2338 target = 0.020812 restraints weight = 179739.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2390 r_free = 0.2390 target = 0.022225 restraints weight = 57474.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2430 r_free = 0.2430 target = 0.023254 restraints weight = 32273.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.023991 restraints weight = 22110.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2479 r_free = 0.2479 target = 0.024500 restraints weight = 16919.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   7557  Z= 0.113
  Angle     :  0.632  11.995  10293  Z= 0.307
  Chirality :  0.040   0.263   1114
  Planarity :  0.004   0.046   1298
  Dihedral  :  8.023  86.642   1004
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.58 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.28), residues: 910
  helix:  2.71 (0.22), residues: 525
  sheet:  0.57 (0.56), residues: 98
  loop :  0.30 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 403 
 TYR   0.017   0.001   TYR C 140 
 PHE   0.017   0.001   PHE E 418 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7553)
  covalent geometry    : angle       0.63224 (10293)
  hydrogen bonds       : bond        0.02774 (  471)
  hydrogen bonds       : angle       4.30504 ( 1340)
  Misc. bond           : bond        0.06043 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9764 (t0) cc_final: 0.9538 (t0)
REVERT: A   94 ASP cc_start: 0.9297 (t0) cc_final: 0.8812 (t0)
REVERT: B   21 ASP cc_start: 0.9066 (p0) cc_final: 0.8140 (p0)
REVERT: B   22 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: B   26 GLU cc_start: 0.9293 (tp30) cc_final: 0.9068 (tp30)
REVERT: B  121 GLU cc_start: 0.9157 (tp30) cc_final: 0.8717 (tp30)
REVERT: B  127 GLN cc_start: 0.9451 (tt0) cc_final: 0.8634 (tm-30)
REVERT: B  131 GLN cc_start: 0.9446 (mm110) cc_final: 0.9037 (mm110)
REVERT: C   68 ASN cc_start: 0.9559 (t0) cc_final: 0.9339 (t0)
REVERT: D   22 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: D   26 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9038 (mm-30)
REVERT: D   55 MET cc_start: 0.9351 (mmp) cc_final: 0.8986 (mmp)
REVERT: D   99 ASP cc_start: 0.8935 (t0) cc_final: 0.8450 (t0)
REVERT: D  127 GLN cc_start: 0.9790 (tt0) cc_final: 0.9277 (tm-30)
REVERT: D  132 LYS cc_start: 0.9667 (mtpp) cc_final: 0.9346 (mtmm)
REVERT: E  124 MET cc_start: 0.7735 (mmm) cc_final: 0.7140 (mmm)
REVERT: E  384 MET cc_start: 0.9725 (ttm) cc_final: 0.9498 (ttm)
REVERT: E  392 TRP cc_start: 0.9221 (m100) cc_final: 0.8549 (m100)
REVERT: E  396 MET cc_start: 0.9165 (tpp) cc_final: 0.8804 (tpp)
  outliers start: 7
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0964
  time to fit residues: 11.3763
Evaluate side-chains
  82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.030580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2334 r_free = 0.2334 target = 0.020718 restraints weight = 171349.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2387 r_free = 0.2387 target = 0.022121 restraints weight = 57236.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2427 r_free = 0.2427 target = 0.023142 restraints weight = 32297.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2455 r_free = 0.2455 target = 0.023857 restraints weight = 22154.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2477 r_free = 0.2477 target = 0.024384 restraints weight = 17014.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.2457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.5449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   7557  Z= 0.114
  Angle     :  0.647  12.027  10293  Z= 0.314
  Chirality :  0.041   0.279   1114
  Planarity :  0.004   0.045   1298
  Dihedral  :  8.015  86.227   1004
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 15.84 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.28), residues: 910
  helix:  2.65 (0.22), residues: 525
  sheet:  0.58 (0.56), residues: 98
  loop :  0.31 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG E 403 
 TYR   0.017   0.001   TYR C 140 
 PHE   0.016   0.001   PHE E 418 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7553)
  covalent geometry    : angle       0.64713 (10293)
  hydrogen bonds       : bond        0.02842 (  471)
  hydrogen bonds       : angle       4.31676 ( 1340)
  Misc. bond           : bond        0.06269 (    4)

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.9763 (t0) cc_final: 0.9530 (t0)
REVERT: A   94 ASP cc_start: 0.9294 (t0) cc_final: 0.8808 (t0)
REVERT: B   21 ASP cc_start: 0.9056 (p0) cc_final: 0.8126 (p0)
REVERT: B   22 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8606 (mm-30)
REVERT: B   26 GLU cc_start: 0.9295 (tp30) cc_final: 0.9076 (tp30)
REVERT: B   73 ASP cc_start: 0.9307 (m-30) cc_final: 0.9032 (t0)
REVERT: B  121 GLU cc_start: 0.9171 (tp30) cc_final: 0.8734 (tp30)
REVERT: B  127 GLN cc_start: 0.9458 (tt0) cc_final: 0.8653 (tm-30)
REVERT: B  131 GLN cc_start: 0.9450 (mm110) cc_final: 0.9119 (mm110)
REVERT: C   32 MET cc_start: 0.9544 (ttm) cc_final: 0.8996 (mtp)
REVERT: C   68 ASN cc_start: 0.9554 (t0) cc_final: 0.9336 (t0)
REVERT: D   22 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: D   26 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: D   55 MET cc_start: 0.9354 (mmp) cc_final: 0.8991 (mmp)
REVERT: D   71 PHE cc_start: 0.9584 (m-80) cc_final: 0.9325 (m-80)
REVERT: D   99 ASP cc_start: 0.8931 (t0) cc_final: 0.8467 (t0)
REVERT: D  127 GLN cc_start: 0.9793 (tt0) cc_final: 0.9284 (tm-30)
REVERT: D  132 LYS cc_start: 0.9668 (mtpp) cc_final: 0.9344 (mtmm)
REVERT: E  124 MET cc_start: 0.7742 (mmm) cc_final: 0.7166 (mmm)
REVERT: E  384 MET cc_start: 0.9726 (ttm) cc_final: 0.9505 (ttm)
REVERT: E  396 MET cc_start: 0.9177 (tpp) cc_final: 0.8819 (tpp)
  outliers start: 5
  outliers final: 5
  residues processed: 80
  average time/residue: 0.0937
  time to fit residues: 10.1906
Evaluate side-chains
  80 residues out of total 767 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 ASP
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain C residue  126 ASP
Chi-restraints excluded: chain D residue    4 THR
Chi-restraints excluded: chain E residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 44 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 87 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 35 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.030301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2311 r_free = 0.2311 target = 0.020209 restraints weight = 215746.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2365 r_free = 0.2365 target = 0.021630 restraints weight = 63274.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2407 r_free = 0.2407 target = 0.022671 restraints weight = 34828.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2437 r_free = 0.2437 target = 0.023423 restraints weight = 23589.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2458 r_free = 0.2458 target = 0.023945 restraints weight = 17990.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2434
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2431 r_free = 0.2431    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2431 r_free = 0.2431    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8911
moved from start:          0.5506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   7557  Z= 0.129
  Angle     :  0.651  12.096  10293  Z= 0.315
  Chirality :  0.041   0.270   1114
  Planarity :  0.004   0.044   1298
  Dihedral  :  8.002  87.224   1004
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 15.84 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.29), residues: 910
  helix:  2.76 (0.23), residues: 521
  sheet:  0.56 (0.56), residues: 98
  loop :  0.26 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 403 
 TYR   0.017   0.001   TYR C 140 
 PHE   0.014   0.001   PHE E 418 
 TRP   0.010   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7553)
  covalent geometry    : angle       0.65121 (10293)
  hydrogen bonds       : bond        0.02798 (  471)
  hydrogen bonds       : angle       4.32947 ( 1340)
  Misc. bond           : bond        0.07620 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1573.49 seconds
wall clock time: 27 minutes 54.85 seconds (1674.85 seconds total)